Variant report

Variant	rs12731254
Chromosome Location	chr1:224019389-224019390
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224017359..224022811-chr1:224031085..224036329,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10799327	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915882	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915892	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10915917	0.93[EUR][1000 genomes]
rs10915946	0.89[EUR][1000 genomes]
rs10915948	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10915950	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10915956	0.89[EUR][1000 genomes]
rs1124943	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11801971	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11802505	0.90[EUR][1000 genomes]
rs11806886	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12021759	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12021785	0.93[EUR][1000 genomes]
rs12024535	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12026098	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12026835	0.93[EUR][1000 genomes]
rs12027539	0.93[EUR][1000 genomes]
rs12030094	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12038299	0.86[EUR][1000 genomes]
rs12040633	0.88[EUR][1000 genomes]
rs12042503	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12045776	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730520	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12745879	0.88[EUR][1000 genomes]
rs12747926	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17559050	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17559134	0.90[ASN][1000 genomes]
rs17599	0.82[EUR][1000 genomes]
rs2014441	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126389	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2169459	0.91[EUR][1000 genomes]
rs34124959	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35634773	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856161	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653644	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653645	0.93[EUR][1000 genomes]
rs4653775	0.82[EUR][1000 genomes]
rs56280097	0.89[EUR][1000 genomes]
rs59866505	0.88[EUR][1000 genomes]
rs61823593	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61823594	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61823595	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61824002	0.86[EUR][1000 genomes]
rs61824006	0.80[EUR][1000 genomes]
rs6658752	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677956	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6678103	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6688246	0.93[EUR][1000 genomes]
rs6693324	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6702843	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs723999	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs745697	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7516059	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519753	0.93[EUR][1000 genomes]
rs7533614	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7554109	0.93[EUR][1000 genomes]
rs9728094	0.83[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	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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 target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription 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 target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:224002200-224020200	Weak transcription	Placenta	Placenta
4	chr1:224002200-224020200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:224007000-224024000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:224007800-224020200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:224008000-224019800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:224008200-224019400	Weak transcription	Hela-S3	cervix
9	chr1:224008600-224019400	Weak transcription	A549	lung
10	chr1:224008800-224020200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:224009000-224019400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:224009000-224019400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:224009000-224020400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:224009200-224019600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:224009200-224020400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:224009400-224019400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:224009400-224019800	Weak transcription	HSMM	muscle
18	chr1:224009400-224019800	Weak transcription	NHDF-Ad	bronchial
19	chr1:224009400-224020200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:224009400-224023800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:224010200-224026400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:224011000-224020200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:224011200-224019400	Weak transcription	NH-A	brain
24	chr1:224011200-224019400	Weak transcription	Osteobl	bone
25	chr1:224011400-224019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:224013800-224019400	Weak transcription	Fetal Lung	lung
27	chr1:224013800-224019400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:224013800-224021600	Weak transcription	Ovary	ovary
29	chr1:224014000-224019400	Weak transcription	Brain Anterior Caudate	brain
30	chr1:224014000-224019400	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:224014000-224019800	Weak transcription	Adipose Nuclei	Adipose
32	chr1:224014000-224020200	Weak transcription	Liver	Liver
33	chr1:224014000-224020200	Weak transcription	Esophagus	oesophagus
34	chr1:224014200-224019400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:224014200-224019800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:224014200-224019800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:224014200-224020200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:224014200-224020200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:224014200-224020400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:224014200-224021400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:224014200-224023400	Weak transcription	Thymus	Thymus
42	chr1:224014200-224023400	Weak transcription	Dnd41	blood
43	chr1:224014200-224024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:224014400-224020400	Weak transcription	Fetal Thymus	thymus
45	chr1:224014600-224019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:224014600-224019800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:224015000-224019400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:224015000-224019400	Weak transcription	Small Intestine	intestine
49	chr1:224015000-224019600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:224015000-224019600	Weak transcription	Fetal Heart	heart

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