Variant report

Variant	rs12241031
Chromosome Location	chr10:52305286-52305287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52305032..52307353-chr10:52341275..52344217,2	K562	blood:
2	chr10:52304249..52305900-chr10:52382183..52384834,2	MCF-7	breast:
3	chr10:52305141..52307249-chr10:52308669..52310332,3	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11006134	0.89[AFR][1000 genomes]
rs12253262	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12259463	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59183272	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131425	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52296800-52306000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr10:52297400-52306000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:52299000-52310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:52299200-52305800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:52299200-52310200	Weak transcription	Pancreas	Pancrea
9	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:52300600-52310200	Weak transcription	Placenta	Placenta
11	chr10:52300800-52310800	Weak transcription	Gastric	stomach
12	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
13	chr10:52301400-52306000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr10:52301400-52308600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:52301600-52306000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr10:52301600-52309200	Weak transcription	Ovary	ovary
17	chr10:52301600-52310200	Weak transcription	Left Ventricle	heart
18	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:52302400-52306000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr10:52302600-52306000	Enhancers	Primary T cells from cord blood	blood
21	chr10:52302800-52306000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr10:52303200-52310200	Weak transcription	Fetal Lung	lung
23	chr10:52303200-52310200	Weak transcription	Stomach Mucosa	stomach
24	chr10:52303200-52312200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:52303400-52309400	Weak transcription	Liver	Liver
26	chr10:52303400-52310200	Weak transcription	Spleen	Spleen
27	chr10:52303400-52310800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:52303400-52312200	Weak transcription	Adipose Nuclei	Adipose
29	chr10:52303400-52314000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:52303800-52306000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr10:52303800-52306000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr10:52304000-52305800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr10:52304000-52306000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:52304000-52306000	Enhancers	Fetal Intestine Small	intestine
35	chr10:52304000-52312000	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:52304200-52305600	Transcr. at gene 5' and 3'	K562	blood
37	chr10:52304200-52305800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr10:52304200-52306000	Enhancers	Brain Cingulate Gyrus	brain
39	chr10:52304400-52305400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr10:52304400-52305600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr10:52304400-52305800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr10:52304400-52305800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr10:52304400-52312000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:52304600-52305600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr10:52304600-52305600	Enhancers	Brain Hippocampus Middle	brain
46	chr10:52304600-52305800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:52304600-52305800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr10:52304600-52306000	Enhancers	Duodenum Mucosa	Duodenum
49	chr10:52304600-52306000	Enhancers	Fetal Heart	heart
50	chr10:52304600-52306000	Enhancers	Fetal Thymus	thymus

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