Variant report

Variant	rs11253290
Chromosome Location	chr10:686197-686198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:684852..686965-chr10:1094186..1096344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047056	Chromatin interaction
ENSG00000067064	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10752016	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10904534	0.88[ASN][1000 genomes]
rs10904537	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11253283	0.95[EUR][1000 genomes]
rs11253284	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11253289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11253291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253292	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11253293	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11253308	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11253315	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11253316	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17136372	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2034851	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28971758	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3750730	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750731	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3853287	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3853288	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3853290	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4369323	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4880737	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4881499	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4881500	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4881503	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4881504	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59280971	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61676960	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61833033	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs705486	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7076929	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7077311	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7919597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883728	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046313	chr10:224406-691123	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv540385	chr10:224406-691123	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1036501	chr10:224406-775824	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1052660	chr10:224406-785929	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1043752	chr10:224406-789665	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv916363	chr10:224406-816628	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv1035580	chr10:248463-832240	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv540392	chr10:248463-832240	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv549751	chr10:313304-734229	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1050252	chr10:375035-839594	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv540397	chr10:375035-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv1036348	chr10:387880-817037	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv1035712	chr10:436747-714987	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
16	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
17	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
18	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
19	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
20	nsv868946	chr10:503401-816628	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
21	nsv1039849	chr10:535309-829217	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
22	nsv915560	chr10:536704-816628	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
23	nsv916839	chr10:536707-817076	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
24	nsv894707	chr10:552355-752193	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
25	nsv1044857	chr10:577396-856059	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
26	nsv540402	chr10:577396-856059	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
27	nsv528733	chr10:577444-838378	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
28	nsv1036675	chr10:600206-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
29	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
30	esv1801137	chr10:626412-735901	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
31	nsv894713	chr10:626782-687569	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv894714	chr10:626782-734229	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
33	nsv1042115	chr10:641343-825145	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
34	nsv540405	chr10:641343-825145	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
35	nsv549764	chr10:671495-704460	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
36	nsv825205	chr10:677475-804402	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:672000-700000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:672200-690600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:672600-695800	Weak transcription	NHLF	lung
4	chr10:673600-687400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:678800-686600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:679400-686800	Weak transcription	Spleen	Spleen
7	chr10:679800-687600	Enhancers	Brain Cingulate Gyrus	brain
8	chr10:680200-690600	Weak transcription	Aorta	Aorta
9	chr10:680400-686400	Weak transcription	Gastric	stomach
10	chr10:680400-687200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:680400-688400	Weak transcription	Stomach Mucosa	stomach
12	chr10:680400-690400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:680400-690600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr10:680400-690600	Weak transcription	Fetal Lung	lung
15	chr10:681200-688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:681800-687200	Weak transcription	Fetal Muscle Leg	muscle
17	chr10:681800-688400	Weak transcription	Right Atrium	heart
18	chr10:681800-688600	Weak transcription	Psoas Muscle	Psoas
19	chr10:681800-690800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:681800-696200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:682400-690800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:683000-686200	Enhancers	Brain Anterior Caudate	brain
23	chr10:683000-696000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:683200-686600	Enhancers	Brain Hippocampus Middle	brain
25	chr10:683600-688400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:683600-688400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:684000-687200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:684000-690600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:684200-700000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr10:684800-686200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:684800-686600	Enhancers	Brain Angular Gyrus	brain
32	chr10:684800-687600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr10:685000-686200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:685000-686200	Enhancers	Left Ventricle	heart
35	chr10:685000-686600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr10:685000-688400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr10:685200-686400	Enhancers	Fetal Brain Male	brain
38	chr10:685200-687000	Enhancers	Esophagus	oesophagus
39	chr10:685200-690200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:685400-688400	Weak transcription	Lung	lung
41	chr10:685600-686800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr10:685600-687000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:685600-690400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:685600-690800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:685600-699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:685800-686200	Enhancers	Pancreas	Pancrea
47	chr10:685800-690400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr10:685800-695200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr10:686000-686200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr10:686000-686400	Enhancers	Brain Substantia Nigra	brain

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