Variant report

Variant	rs3772525
Chromosome Location	chr3:105441890-105441891
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	chr3:105435086..105438281-chr3:105439598..105442695,3	MCF-7	breast:
2	chr3:105438428..105441312-chr3:105441392..105443154,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12054270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487349	0.90[ASN][1000 genomes]
rs12493071	0.90[ASN][1000 genomes]
rs12493771	0.84[ASN][1000 genomes]
rs12632595	0.81[AFR][1000 genomes]
rs1443100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851707	0.90[ASN][1000 genomes]
rs1814078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1867194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2028598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055558	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2055559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2120103	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs2120104	0.85[ASN][1000 genomes]
rs2301028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34360428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35909361	0.87[ASN][1000 genomes]
rs3772517	0.93[ASN][1000 genomes]
rs3772522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821490	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4431143	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4469007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4894956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62255570	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255571	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255572	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255573	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255575	0.90[ASN][1000 genomes]
rs62256353	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62258160	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62261460	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261487	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261489	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261491	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261492	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261493	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261495	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261496	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261497	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261498	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261499	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261538	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261539	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62263056	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62263057	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62263059	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62263169	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62263170	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264260	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7628896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641527	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7650046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs964173	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9657903	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9657924	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs971109	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849559	0.85[ASN][1000 genomes]
rs9856147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv877307	chr3:105373836-105465189	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv591242	chr3:105373836-105470134	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv591243	chr3:105438320-105470134	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv591245	chr3:105438806-105469882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
2	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
4	chr3:105407800-105457800	Weak transcription	HepG2	liver
5	chr3:105417400-105443400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:105420800-105445600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:105421200-105465400	Weak transcription	Colonic Mucosa	Colon
8	chr3:105421400-105443000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:105425400-105442400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:105432800-105463800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:105433600-105465600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:105433800-105445400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:105434400-105446600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:105434800-105463800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:105438800-105442000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:105438800-105442400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:105438800-105464000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:105438800-105465400	Weak transcription	Fetal Heart	heart
19	chr3:105439000-105442000	Weak transcription	Fetal Brain Female	brain
20	chr3:105439000-105442400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:105439000-105442800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:105439000-105445400	Weak transcription	Fetal Lung	lung
23	chr3:105439000-105446200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:105439000-105447200	Weak transcription	HSMM	muscle
25	chr3:105439000-105450600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:105439000-105457800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:105439000-105461600	Weak transcription	Dnd41	blood
28	chr3:105439000-105464000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:105439000-105464200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:105439000-105465400	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:105439000-105465800	Weak transcription	NHLF	lung
32	chr3:105439000-105466200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:105439000-105466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:105439000-105471200	Weak transcription	Fetal Thymus	thymus
35	chr3:105439000-105471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:105439000-105471400	Weak transcription	HMEC	breast
37	chr3:105439000-105471600	Weak transcription	Fetal Brain Male	brain
38	chr3:105439000-105475800	Weak transcription	Esophagus	oesophagus
39	chr3:105439000-105477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:105439000-105477400	Weak transcription	Lung	lung
41	chr3:105439000-105477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:105439200-105442000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:105439200-105442200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:105439200-105443200	Weak transcription	Brain Germinal Matrix	brain
45	chr3:105439200-105444400	Weak transcription	NH-A	brain
46	chr3:105439200-105444800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:105439200-105444800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:105439200-105444800	Weak transcription	HSMMtube	muscle
49	chr3:105439200-105445400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:105439200-105445400	Weak transcription	Gastric	stomach

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