Variant report

Variant	rs6656888
Chromosome Location	chr1:78481045-78481046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1001070	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes]
rs1001103	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs1001104	0.90[AMR][1000 genomes]
rs10437022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873956	0.89[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs10873960	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873962	0.80[AMR][1000 genomes]
rs10873963	0.82[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs11162400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162403	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162406	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1166697	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166701	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166704	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1166705	0.85[AMR][1000 genomes]
rs1166706	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1166707	0.88[AMR][1000 genomes]
rs1166709	0.81[CHB][hapmap]
rs11805735	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11807240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146104	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12404652	0.82[MEX][hapmap]
rs12405212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12409561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12723748	0.82[AMR][1000 genomes]
rs1335481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1536160	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539737	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1555798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1616949	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17382996	1.00[CEU][hapmap]
rs17383213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17387365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1855704	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs1970210	0.80[AMR][1000 genomes]
rs1971368	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1984298	0.82[MEX][hapmap]
rs2136682	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2154138	0.89[ASW][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs2274257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4370803	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4372306	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631748	0.89[AMR][1000 genomes]
rs4949828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs504388	0.83[AMR][1000 genomes]
rs57421725	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs628451	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs638335	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs6424640	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6424660	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6424664	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6424668	0.84[AMR][1000 genomes]
rs661038	0.88[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs664818	0.83[AMR][1000 genomes]
rs6677890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes]
rs6686230	0.86[AMR][1000 genomes]
rs684579	0.82[AMR][1000 genomes]
rs7417104	0.81[CHB][hapmap]
rs750720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514007	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes]
rs7538210	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9324166	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9659938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9661193	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9730688	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv1801396	chr1:78468094-78492221	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78448800-78488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:78454200-78485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:78470800-78487800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:78471000-78487400	Weak transcription	Lung	lung
5	chr1:78471200-78486400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:78471600-78483000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:78471600-78483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:78471600-78483800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:78471600-78487000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:78471800-78482000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:78472000-78484800	Weak transcription	Colonic Mucosa	Colon
12	chr1:78472000-78487000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:78472200-78484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:78472400-78483200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:78472400-78486800	Weak transcription	Fetal Thymus	thymus
16	chr1:78472800-78481600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:78472800-78482000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:78472800-78486400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:78473800-78487000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:78474000-78483200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:78474000-78486800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:78474000-78486800	Weak transcription	Pancreas	Pancrea
23	chr1:78474200-78482600	Weak transcription	NHEK	skin
24	chr1:78474200-78483600	Weak transcription	HMEC	breast
25	chr1:78474200-78484800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:78474200-78486000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:78474200-78486600	Weak transcription	Primary B cells from cord blood	blood
28	chr1:78474200-78486800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:78474400-78486400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:78475200-78484000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:78475200-78495600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:78475800-78481600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:78475800-78483400	Weak transcription	Dnd41	blood
34	chr1:78475800-78487800	Weak transcription	Psoas Muscle	Psoas
35	chr1:78475800-78491400	Weak transcription	Ovary	ovary
36	chr1:78476200-78484800	Weak transcription	Small Intestine	intestine
37	chr1:78476600-78486000	Weak transcription	Brain Anterior Caudate	brain
38	chr1:78476800-78486200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:78476800-78486600	Weak transcription	Brain Substantia Nigra	brain
40	chr1:78477000-78488400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:78477200-78481600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:78477400-78494000	Weak transcription	Aorta	Aorta
43	chr1:78477600-78481400	Weak transcription	Gastric	stomach
44	chr1:78478400-78482000	Strong transcription	HSMMtube	muscle
45	chr1:78478400-78482800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:78478400-78485000	Strong transcription	Osteobl	bone
47	chr1:78478600-78481200	Genic enhancers	HUVEC	blood vessel
48	chr1:78478600-78481800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:78478600-78482000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:78478600-78482200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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