Variant report

Variant	rs7628896
Chromosome Location	chr3:105435980-105435981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:105431222..105434203-chr3:105434765..105437080,2	MCF-7	breast:
2	chr3:105435161..105438047-chr3:105586543..105588230,2	MCF-7	breast:
3	chr3:105435086..105438281-chr3:105439598..105442695,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12054270	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	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851553	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851673	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851707	0.90[ASN][1000 genomes]
rs1814078	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1867194	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2028598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028599	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	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2120103	0.90[AMR][1000 genomes]
rs2120104	0.85[ASN][1000 genomes]
rs2301028	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301034	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213928	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	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821490	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4431143	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4469007	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4894956	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	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619706	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631219	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	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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs971109	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849559	0.85[ASN][1000 genomes]
rs9856147	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	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

No data

Chromatin state (count:119 , 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	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:105378600-105438600	Weak transcription	Spleen	Spleen
6	chr3:105379000-105437400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:105379200-105440400	Weak transcription	Thymus	Thymus
8	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
9	chr3:105394200-105438800	Weak transcription	NHEK	skin
10	chr3:105396000-105437200	Weak transcription	Psoas Muscle	Psoas
11	chr3:105396000-105437400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105396000-105438200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:105396000-105438400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:105400000-105437200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:105405200-105437200	Weak transcription	NHLF	lung
16	chr3:105407800-105457800	Weak transcription	HepG2	liver
17	chr3:105408400-105440400	Weak transcription	A549	lung
18	chr3:105409000-105441600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:105410800-105437600	Weak transcription	Fetal Heart	heart
20	chr3:105412400-105437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:105412400-105441600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:105412600-105437400	Weak transcription	Dnd41	blood
23	chr3:105415600-105438000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:105417200-105436800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:105417400-105443400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:105419200-105439200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:105420800-105445600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:105421200-105436400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:105421200-105436600	Weak transcription	Brain Germinal Matrix	brain
30	chr3:105421200-105437000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:105421200-105437200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:105421200-105437200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:105421200-105437400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:105421200-105437600	Weak transcription	Brain Anterior Caudate	brain
35	chr3:105421200-105438000	Weak transcription	Aorta	Aorta
36	chr3:105421200-105438200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:105421200-105438800	Weak transcription	Esophagus	oesophagus
38	chr3:105421200-105441800	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:105421200-105465400	Weak transcription	Colonic Mucosa	Colon
40	chr3:105421400-105436800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:105421400-105436800	Weak transcription	Ovary	ovary
42	chr3:105421400-105437400	Weak transcription	Brain Angular Gyrus	brain
43	chr3:105421400-105437400	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:105421400-105438000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:105421400-105443000	Weak transcription	Fetal Intestine Small	intestine
46	chr3:105421600-105437200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:105422000-105441400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:105422600-105437200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:105423000-105436800	Weak transcription	HUVEC	blood vessel
50	chr3:105423000-105436800	Weak transcription	Monocytes-CD14+_RO01746	blood

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