Variant report

Variant	rs6794956
Chromosome Location	chr3:178743220-178743221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178736144..178738008-chr3:178740817..178744400,3	K562	blood:
2	chr3:178743208..178744872-chr3:178748172..178749949,2	K562	blood:
3	chr3:178743217..178745083-chr3:178864764..178866616,2	K562	blood:
4	chr3:178741511..178744382-chr3:178747703..178750492,2	K562	blood:
5	chr3:178742128..178744484-chr3:178786941..178789605,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172667	Chromatin interaction
ENSG00000121879	Chromatin interaction
ENSG00000229102	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11711320	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720081	0.87[EUR][1000 genomes]
rs1542	0.83[ASN][1000 genomes]
rs4245914	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4279147	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280676	0.87[EUR][1000 genomes]
rs4315724	0.87[EUR][1000 genomes]
rs4337680	0.87[EUR][1000 genomes]
rs4377525	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4395442	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4417911	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425305	0.88[ASN][1000 genomes]
rs4469018	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501160	0.87[EUR][1000 genomes]
rs4505756	0.87[EUR][1000 genomes]
rs4522816	0.85[EUR][1000 genomes]
rs4525914	0.84[EUR][1000 genomes]
rs4552405	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4579062	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626139	0.87[EUR][1000 genomes]
rs4632588	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637331	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955796	0.87[EUR][1000 genomes]
rs4955802	0.85[EUR][1000 genomes]
rs4955807	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955810	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115013	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56154408	0.85[EUR][1000 genomes]
rs6443607	0.84[EUR][1000 genomes]
rs6443614	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443617	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6443618	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6772028	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784495	0.86[AMR][1000 genomes]
rs6789706	0.83[EUR][1000 genomes]
rs6790867	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793769	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794165	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6795238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800015	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7429173	0.87[EUR][1000 genomes]
rs7612363	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7639391	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643052	0.85[EUR][1000 genomes]
rs7651510	0.87[EUR][1000 genomes]
rs7652668	0.86[EUR][1000 genomes]
rs7652946	0.87[EUR][1000 genomes]
rs9830482	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831543	0.83[ASN][1000 genomes]
rs9835752	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835765	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846511	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9860318	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860749	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878734	0.97[ASN][1000 genomes]
rs9879637	0.87[EUR][1000 genomes]
rs9880749	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1009143	chr3:178731525-178783915	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv1799481	chr3:178733212-178782021	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178716400-178755000	Weak transcription	Pancreas	Pancrea
2	chr3:178717400-178744400	Weak transcription	HMEC	breast
3	chr3:178722200-178751600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:178723400-178749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:178723800-178754200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:178731400-178744400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:178732600-178744200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:178733400-178751400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:178733800-178754600	Weak transcription	Lung	lung
10	chr3:178734000-178755200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:178734000-178755400	Weak transcription	HepG2	liver
12	chr3:178735000-178763800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:178735600-178744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:178735600-178745600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:178735800-178751600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:178736200-178744400	Weak transcription	NHLF	lung
17	chr3:178738000-178764000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:178738200-178744400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:178738200-178751600	Weak transcription	Stomach Mucosa	stomach
20	chr3:178738400-178745000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:178738600-178744400	Weak transcription	Fetal Lung	lung
22	chr3:178738600-178744400	Weak transcription	Small Intestine	intestine
23	chr3:178738600-178745200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:178738600-178745600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:178738600-178745600	Weak transcription	Thymus	Thymus
26	chr3:178738600-178748400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:178738600-178751600	Weak transcription	Adipose Nuclei	Adipose
28	chr3:178738600-178751600	Weak transcription	Gastric	stomach
29	chr3:178738600-178751600	Weak transcription	Ovary	ovary
30	chr3:178738600-178754800	Weak transcription	Spleen	Spleen
31	chr3:178738600-178755000	Weak transcription	Aorta	Aorta
32	chr3:178738600-178757000	Weak transcription	Fetal Stomach	stomach
33	chr3:178738800-178744400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:178738800-178745200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:178738800-178745400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:178738800-178745600	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:178738800-178745600	Weak transcription	Brain Substantia Nigra	brain
38	chr3:178738800-178748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:178738800-178754400	Weak transcription	Psoas Muscle	Psoas
40	chr3:178738800-178755800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:178738800-178757000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:178739400-178751400	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:178739600-178744400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:178739600-178744600	Weak transcription	Fetal Kidney	kidney
45	chr3:178739600-178745400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:178739600-178745600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:178739600-178747000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:178739600-178755800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:178739800-178743800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:178739800-178744200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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