Variant report

Variant	rs1075739
Chromosome Location	chr3:105441133-105441134
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	chr3:105438428..105441312-chr3:105441392..105443154,2	K562	blood:
2	chr3:105435086..105438281-chr3:105439598..105442695,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10460808	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs10511246	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11921710	0.80[ASN][1000 genomes]
rs12489983	0.85[CEU][hapmap]
rs12633654	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639271	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561922	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844736	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs16851523	1.00[CEU][hapmap];0.94[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]
rs16851539	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];0.99[ASN][1000 genomes]
rs16851563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867192	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1947000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992521	0.81[EUR][1000 genomes]
rs2089091	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2197208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197209	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301036	0.81[EUR][1000 genomes]
rs3772540	0.82[CEU][hapmap]
rs3821489	0.85[CEU][hapmap]
rs57520912	0.80[ASN][1000 genomes]
rs58340800	0.80[ASN][1000 genomes]
rs59534462	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59611997	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60295307	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60619938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437620	0.81[ASN][1000 genomes]
rs6437621	0.81[ASN][1000 genomes]
rs73854891	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73854894	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73857222	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7629357	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7648842	0.81[ASN][1000 genomes]
rs9631436	0.80[ASN][1000 genomes]
rs9789988	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826886	0.81[ASN][1000 genomes]
rs9846534	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9874600	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[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:112 , 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	chr3:105409000-105441600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:105412400-105441600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:105417400-105443400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:105420800-105445600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:105421200-105441800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:105421200-105465400	Weak transcription	Colonic Mucosa	Colon
11	chr3:105421400-105443000	Weak transcription	Fetal Intestine Small	intestine
12	chr3:105422000-105441400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:105425400-105442400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:105429800-105441200	Strong transcription	Osteobl	bone
15	chr3:105432200-105441600	Strong transcription	Left Ventricle	heart
16	chr3:105432800-105463800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:105433600-105465600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:105433800-105445400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:105434400-105446600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:105434800-105463800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:105438400-105441800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:105438800-105442000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:105438800-105442400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:105438800-105464000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:105438800-105465400	Weak transcription	Fetal Heart	heart
26	chr3:105439000-105441400	Weak transcription	Primary B cells from cord blood	blood
27	chr3:105439000-105441400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:105439000-105441600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:105439000-105441800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:105439000-105441800	Weak transcription	Brain Anterior Caudate	brain
31	chr3:105439000-105442000	Weak transcription	Fetal Brain Female	brain
32	chr3:105439000-105442400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:105439000-105442800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:105439000-105445400	Weak transcription	Fetal Lung	lung
35	chr3:105439000-105446200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:105439000-105447200	Weak transcription	HSMM	muscle
37	chr3:105439000-105450600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:105439000-105457800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:105439000-105461600	Weak transcription	Dnd41	blood
40	chr3:105439000-105464000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:105439000-105464200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:105439000-105465400	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:105439000-105465800	Weak transcription	NHLF	lung
44	chr3:105439000-105466200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:105439000-105466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:105439000-105471200	Weak transcription	Fetal Thymus	thymus
47	chr3:105439000-105471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:105439000-105471400	Weak transcription	HMEC	breast
49	chr3:105439000-105471600	Weak transcription	Fetal Brain Male	brain
50	chr3:105439000-105475800	Weak transcription	Esophagus	oesophagus

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