Variant report

Variant	rs2177461
Chromosome Location	chr1:85861976-85861977
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1001604	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1006989	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs10489513	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10747318	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs10782549	0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs10873701	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs10873702	0.81[AFR][1000 genomes]
rs11161606	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161610	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146379	0.83[EUR][1000 genomes]
rs12044537	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12047422	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12124170	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12125557	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140103	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357635	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs1498373	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498375	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523994	0.92[YRI][hapmap]
rs1523995	0.85[AFR][1000 genomes]
rs1554597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1608537	0.88[AFR][1000 genomes]
rs173026	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs18582	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1884139	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965876	0.88[AFR][1000 genomes]
rs1975755	0.87[YRI][hapmap]
rs2011825	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2012683	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016104	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs2207368	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300637	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs233047	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233050	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233053	0.88[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233054	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233057	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233058	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233059	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233060	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233061	0.84[EUR][1000 genomes]
rs233062	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233066	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233067	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233068	0.85[EUR][1000 genomes]
rs233069	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233071	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233072	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs233074	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233091	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233093	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233095	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs233097	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs233099	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233108	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233109	0.84[EUR][1000 genomes]
rs233112	0.84[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs233113	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233114	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233115	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233118	0.84[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs233119	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233120	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233121	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233124	0.84[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs233127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233130	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233131	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233132	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233133	0.84[EUR][1000 genomes]
rs2840319	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2892888	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087894	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3920521	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3949301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs423105	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4428939	0.86[AFR][1000 genomes]
rs4949890	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506082	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs539714	1.00[YRI][hapmap]
rs600098	0.81[YRI][hapmap]
rs6420965	0.86[AFR][1000 genomes]
rs6576761	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6576763	0.88[CEU][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576764	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576765	0.88[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576766	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6576767	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659070	0.81[YRI][hapmap]
rs6657817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671599	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672870	1.00[YRI][hapmap]
rs66811655	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697083	0.95[CEU][hapmap]
rs6704103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67611930	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72724606	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72724608	0.90[AFR][1000 genomes]
rs729655	0.85[AMR][1000 genomes]
rs7515261	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs7539738	0.83[AFR][1000 genomes]
rs7546931	0.80[AFR][1000 genomes]
rs7547571	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs761601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997251	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
2	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
3	chr1:85849400-85863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:85850800-85863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:85852400-85863400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:85852400-85864200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85853800-85864200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:85854600-85862800	Weak transcription	Liver	Liver
9	chr1:85854600-85863400	Weak transcription	HUVEC	blood vessel
10	chr1:85855200-85870000	Weak transcription	Fetal Stomach	stomach
11	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
12	chr1:85858800-85863600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:85859400-85865000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:85860200-85862000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:85860200-85862800	Weak transcription	NHLF	lung
16	chr1:85860400-85862000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:85860600-85862000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:85860600-85862800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:85861000-85862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:85861000-85863600	Weak transcription	HSMM	muscle
21	chr1:85861200-85862200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:85861200-85862800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:85861600-85862000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:85861600-85862000	Strong transcription	NH-A	brain
25	chr1:85861600-85862200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:85861600-85862200	Enhancers	NHDF-Ad	bronchial
27	chr1:85861600-85865800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:85861800-85862000	Enhancers	Rectal Smooth Muscle	rectum
29	chr1:85861800-85862400	Enhancers	Osteobl	bone
30	chr1:85861800-85862600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:85861800-85863000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:85861800-85865800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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