Variant report

Variant	rs1360239
Chromosome Location	chr1:86092393-86092394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10747323	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747324	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs10873711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873718	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs10873719	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs1094353	0.89[AMR][1000 genomes]
rs1094360	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12037294	0.84[EUR][1000 genomes]
rs12405017	0.87[CHD][hapmap]
rs12757797	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs12758966	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1481200	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1764287	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1764295	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1775985	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1775986	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1775987	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1775991	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1775992	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs1775993	0.87[CHD][hapmap];0.81[GIH][hapmap]
rs1999186	0.83[AFR][1000 genomes]
rs2014733	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2014750	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs2026772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026773	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs2026774	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs2389973	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2389974	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2389975	0.84[EUR][1000 genomes]
rs2970548	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes]
rs313723	0.82[AMR][1000 genomes]
rs313724	0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs313725	0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs369999	1.00[CEU][hapmap]
rs381453	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs399547	1.00[CEU][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs401657	0.82[YRI][hapmap]
rs420515	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs425357	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs429040	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs430956	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[YRI][hapmap]
rs432254	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4379699	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs438401	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs444875	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs450953	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs4949913	0.83[YRI][hapmap]
rs4949917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576781	0.83[AFR][1000 genomes]
rs6673975	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs6682235	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs6686719	1.00[CEU][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6694808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521240	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7528385	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7529942	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7533395	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535884	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7547023	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs821378	1.00[ASW][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs821380	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs821382	0.83[AFR][1000 genomes]
rs821383	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs821385	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs821387	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs821388	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs821390	1.00[ASW][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.96[YRI][hapmap]
rs821392	0.92[EUR][1000 genomes]
rs821397	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs821400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs821402	0.93[ASW][hapmap]
rs821403	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs821404	0.82[AFR][1000 genomes]
rs849158	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9324152	1.00[ASW][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.96[YRI][hapmap]
rs9324153	0.93[ASW][hapmap]
rs9651138	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9661608	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9661951	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9701898	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9793556	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86079200-86094400	Weak transcription	Pancreas	Pancrea
2	chr1:86083800-86095200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:86084600-86092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:86085800-86093200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:86087400-86094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:86088200-86094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:86088200-86101800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:86088400-86094200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:86088400-86101400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:86088400-86102000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:86088400-86103000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:86088600-86092400	Weak transcription	Psoas Muscle	Psoas
14	chr1:86088600-86094400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:86088600-86094400	Weak transcription	Left Ventricle	heart
16	chr1:86088600-86094800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:86088600-86094800	Weak transcription	Right Ventricle	heart
18	chr1:86088600-86101800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:86088600-86103000	Weak transcription	NHEK	skin
20	chr1:86088800-86093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:86088800-86093400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:86088800-86094200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:86088800-86094200	Weak transcription	Liver	Liver
24	chr1:86088800-86094400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:86088800-86094400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:86088800-86094400	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:86088800-86094600	Weak transcription	Fetal Intestine Small	intestine
28	chr1:86088800-86094800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:86088800-86094800	Weak transcription	Esophagus	oesophagus
30	chr1:86088800-86101000	Weak transcription	Dnd41	blood
31	chr1:86088800-86101800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:86088800-86101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:86089200-86094200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:86089200-86094200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:86089400-86092400	Weak transcription	HSMMtube	muscle
36	chr1:86089400-86092400	Weak transcription	K562	blood
37	chr1:86089400-86093000	Weak transcription	NHDF-Ad	bronchial
38	chr1:86089400-86093200	Weak transcription	NHLF	lung
39	chr1:86089400-86093600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:86089400-86094200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:86089400-86094400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:86089400-86094400	Weak transcription	Placenta	Placenta
43	chr1:86089400-86094600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:86089400-86094800	Weak transcription	Ovary	ovary
45	chr1:86089400-86102600	Weak transcription	GM12878-XiMat	blood
46	chr1:86089400-86103000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:86089600-86093400	Weak transcription	NH-A	brain
48	chr1:86089600-86094000	Weak transcription	Fetal Stomach	stomach
49	chr1:86089600-86094400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:86090000-86092800	Weak transcription	Primary hematopoietic stem cells	blood

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