Variant report

Variant	rs3767028
Chromosome Location	chr1:78408536-78408537
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001070	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1001103	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1001104	0.80[AMR][1000 genomes]
rs10437022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873956	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10873960	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162403	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162406	0.81[AMR][1000 genomes]
rs1166697	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166702	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];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166704	0.81[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1166705	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1166706	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1166707	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs1166709	0.81[CHB][hapmap]
rs11805735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807240	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146104	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12405212	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];0.96[EUR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723748	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1335481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1536160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539737	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1555798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1616949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1626757	0.82[AMR][1000 genomes]
rs17382996	1.00[CEU][hapmap]
rs17383213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17387365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1855704	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1971368	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2136682	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2154138	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2274257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4370803	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4372306	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949828	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];0.96[EUR][1000 genomes];0.96[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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57421725	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6424650	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424660	0.84[AMR][1000 genomes]
rs6424664	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs661038	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs6656888	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]
rs6659045	0.80[AMR][1000 genomes]
rs6667733	0.80[AMR][1000 genomes]
rs6677890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs7417104	0.81[CHB][hapmap]
rs750720	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];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514007	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs7538210	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7544892	0.80[AMR][1000 genomes]
rs9324166	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9659938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9661193	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9730688	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78356200-78408600	Weak transcription	HMEC	breast
2	chr1:78371600-78413000	Weak transcription	Psoas Muscle	Psoas
3	chr1:78372800-78418600	Weak transcription	Pancreas	Pancrea
4	chr1:78383600-78418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:78387800-78412600	Weak transcription	Fetal Brain Male	brain
6	chr1:78388600-78416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:78388800-78410000	Strong transcription	HSMMtube	muscle
8	chr1:78389000-78414600	Strong transcription	NH-A	brain
9	chr1:78390200-78409800	Weak transcription	NHEK	skin
10	chr1:78392000-78411000	Weak transcription	Brain Anterior Caudate	brain
11	chr1:78392200-78420400	Strong transcription	HSMM	muscle
12	chr1:78392800-78408800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:78393000-78418600	Weak transcription	Lung	lung
14	chr1:78393200-78417400	Weak transcription	Small Intestine	intestine
15	chr1:78393400-78409000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:78393400-78418000	Weak transcription	Stomach Mucosa	stomach
17	chr1:78394000-78411400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:78396200-78414400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr1:78396800-78411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:78396800-78415800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:78396800-78419600	Weak transcription	Ovary	ovary
22	chr1:78397800-78418600	Weak transcription	Spleen	Spleen
23	chr1:78398600-78418400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:78400400-78417200	Weak transcription	Gastric	stomach
25	chr1:78400600-78415800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:78401800-78411800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:78402000-78413000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:78402000-78413000	Weak transcription	Primary T cells from cord blood	blood
29	chr1:78403000-78418800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:78403200-78415800	Weak transcription	Fetal Stomach	stomach
31	chr1:78404200-78408600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:78404400-78412200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:78405000-78410600	Weak transcription	HepG2	liver
34	chr1:78405000-78411600	Strong transcription	NHLF	lung
35	chr1:78405000-78411800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:78405000-78413000	Weak transcription	Colonic Mucosa	Colon
37	chr1:78405000-78418600	Weak transcription	Aorta	Aorta
38	chr1:78405200-78410800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:78405200-78417800	Weak transcription	Fetal Intestine Small	intestine
40	chr1:78405600-78415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:78405800-78410600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:78405800-78412000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:78405800-78414600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:78405800-78416600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
47	chr1:78406000-78411400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:78406000-78414600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:78406000-78420200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:78406000-78426600	Weak transcription	Fetal Heart	heart

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