Variant report

Variant	rs12641291
Chromosome Location	chr4:148753943-148753944
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:148651228..148655944-chr4:148751568..148754818,6	MCF-7	breast:
2	chr4:148753166..148755265-chr4:148757351..148759207,2	MCF-7	breast:
3	chr4:148661332..148664177-chr4:148751893..148754827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10003507	0.82[CEU][hapmap]
rs10004138	0.82[CEU][hapmap]
rs10004792	0.82[CEU][hapmap]
rs10004850	1.00[ASN][1000 genomes]
rs10005192	0.85[CEU][hapmap]
rs10007231	0.89[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10014696	0.82[CEU][hapmap]
rs10018820	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10018903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021936	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10022691	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10023057	0.80[AMR][1000 genomes]
rs10025684	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10026985	0.82[CEU][hapmap]
rs10029385	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10030358	0.82[CEU][hapmap]
rs10030513	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10049932	0.82[CEU][hapmap]
rs10519917	0.85[CEU][hapmap]
rs11099671	0.82[CEU][hapmap]
rs11099672	0.82[CEU][hapmap]
rs11724795	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes]
rs11735412	0.82[CEU][hapmap]
rs11935450	0.85[CEU][hapmap]
rs11935510	0.85[CEU][hapmap]
rs11935620	0.85[CEU][hapmap]
rs11940379	0.82[CEU][hapmap]
rs12331562	0.82[CEU][hapmap]
rs12509618	0.82[CEU][hapmap]
rs12513192	0.82[CEU][hapmap]
rs12647314	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650219	1.00[CEU][hapmap]
rs13116821	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13129325	0.82[CEU][hapmap]
rs13129747	1.00[ASN][1000 genomes]
rs13434396	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1347596	0.82[ASN][1000 genomes]
rs1369958	0.82[CEU][hapmap]
rs1436489	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1436490	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17023870	0.85[CEU][hapmap]
rs17023919	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17024037	0.82[CEU][hapmap]
rs17613979	0.82[CEU][hapmap]
rs17614025	0.82[CEU][hapmap]
rs17676080	0.82[CEU][hapmap]
rs2043644	1.00[CEU][hapmap]
rs28662484	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35115631	1.00[ASN][1000 genomes]
rs3893175	0.82[CEU][hapmap]
rs3990920	0.82[CEU][hapmap]
rs4240338	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4240339	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4240341	0.82[CEU][hapmap]
rs4419463	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4491995	0.82[CEU][hapmap]
rs4571312	0.82[CEU][hapmap]
rs4835103	0.82[CEU][hapmap]
rs4835109	0.82[CEU][hapmap]
rs4835461	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs62330695	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66488204	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818371	0.82[CEU][hapmap]
rs6839440	0.89[ASN][1000 genomes]
rs6840771	0.82[CEU][hapmap]
rs6843392	0.82[CEU][hapmap]
rs6856273	0.82[CEU][hapmap]
rs7655236	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7660508	0.82[CEU][hapmap]
rs7666127	0.82[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs893022	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs893033	0.82[CEU][hapmap]
rs9991741	0.82[CEU][hapmap]
rs9994650	0.82[CEU][hapmap]
rs9995896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995956	0.82[CEU][hapmap]
rs9996108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996209	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9997027	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking 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	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148734600-148761000	Weak transcription	Fetal Kidney	kidney
2	chr4:148737200-148758200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr4:148737800-148755400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:148737800-148757000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:148737800-148782200	Weak transcription	Thymus	Thymus
6	chr4:148741400-148754000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:148743200-148782200	Weak transcription	Fetal Intestine Large	intestine
8	chr4:148743600-148755400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:148746200-148754000	Weak transcription	Brain Substantia Nigra	brain
10	chr4:148746400-148768000	Weak transcription	Fetal Intestine Small	intestine
11	chr4:148747800-148754600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:148749200-148754600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:148749400-148754000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:148749400-148754000	Enhancers	HSMM	muscle
15	chr4:148749400-148754800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr4:148749400-148754800	Enhancers	HMEC	breast
17	chr4:148749400-148758000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:148751400-148755400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:148751400-148757200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:148751400-148776000	Weak transcription	Fetal Stomach	stomach
21	chr4:148752000-148754000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:148752000-148755200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr4:148752200-148754200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:148752200-148755200	ZNF genes & repeats	GM12878-XiMat	blood
25	chr4:148752400-148761200	Weak transcription	Psoas Muscle	Psoas
26	chr4:148752600-148756000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:148752800-148754200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:148752800-148754600	Enhancers	Right Ventricle	heart
29	chr4:148753000-148756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:148753200-148755400	Weak transcription	Lung	lung
31	chr4:148753200-148756000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:148753200-148756000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:148753200-148756000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:148753200-148756400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:148753200-148763600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:148753200-148765800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:148753200-148767800	Weak transcription	Small Intestine	intestine
38	chr4:148753400-148754000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:148753400-148754000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:148753400-148754000	Enhancers	NHLF	lung
41	chr4:148753400-148754200	Weak transcription	Left Ventricle	heart
42	chr4:148753400-148754200	Enhancers	HSMMtube	muscle
43	chr4:148753400-148754400	Enhancers	NHEK	skin
44	chr4:148753400-148754600	Enhancers	NHDF-Ad	bronchial
45	chr4:148753400-148755000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:148753400-148755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:148753400-148755400	Weak transcription	Esophagus	oesophagus
48	chr4:148753400-148756400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr4:148753400-148756600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:148753400-148757200	Weak transcription	Stomach Smooth Muscle	stomach

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