Variant report

Variant	rs6667609
Chromosome Location	chr1:103499049-103499050
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10047106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10493987	1.00[CEU][hapmap]
rs10747433	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10747435	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10782915	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10782916	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10782917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10782920	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10874676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164647	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1337192	1.00[CEU][hapmap]
rs1415350	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463040	1.00[CEU][hapmap]
rs1463044	1.00[CEU][hapmap]
rs1538047	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1538048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1564141	1.00[CEU][hapmap]
rs1676488	1.00[CEU][hapmap]
rs1676492	0.87[AMR][1000 genomes]
rs1676503	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs1676504	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17101127	1.00[CEU][hapmap]
rs17127490	1.00[CEU][hapmap]
rs1763351	1.00[CEU][hapmap]
rs1841834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1966958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2184879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2199553	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2251895	1.00[EUR][1000 genomes]
rs2615976	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615994	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2616000	1.00[CEU][hapmap]
rs2616008	1.00[CEU][hapmap]
rs2616009	1.00[CEU][hapmap]
rs2616013	1.00[CEU][hapmap]
rs2622841	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2622849	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2622861	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2622862	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2622864	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2622867	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2622868	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2786124	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2929161	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2929162	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3102057	1.00[CEU][hapmap]
rs3126212	1.00[CEU][hapmap]
rs3126213	1.00[CEU][hapmap]
rs3126215	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3861743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3908855	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4013869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4357546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4480381	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4908279	0.87[AMR][1000 genomes]
rs6577342	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577353	1.00[CEU][hapmap]
rs6674148	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6700031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7523020	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7523441	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7531081	1.00[CEU][hapmap]
rs7541571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544444	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7544816	1.00[CEU][hapmap]
rs9701540	0.92[EUR][1000 genomes]
rs981961	1.00[CEU][hapmap]
rs992098	1.00[CEU][hapmap]
rs992099	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv871741	chr1:103352451-103517428	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv871078	chr1:103352451-103548497	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv870607	chr1:103362909-103528128	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv870995	chr1:103384610-103548497	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv871372	chr1:103403752-103564540	Strong transcription Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv871067	chr1:103407999-103509323	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv871736	chr1:103409100-103548497	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv871567	chr1:103416690-103499049	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv871657	chr1:103427381-103528128	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv462772	chr1:103438795-103499896	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv546936	chr1:103438795-103499896	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv462783	chr1:103438795-103548497	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv546937	chr1:103438795-103548497	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv462794	chr1:103450196-103539007	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv546938	chr1:103450196-103539007	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv871286	chr1:103455217-103528128	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv871733	chr1:103459537-103509323	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv871071	chr1:103471962-103509323	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv871365	chr1:103476179-103548497	Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv1835970	chr1:103481299-103510756	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103449200-103545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:103460200-103516400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:103475800-103516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:103489200-103516400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:103489600-103506000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:103491600-103503800	Weak transcription	NH-A	brain
7	chr1:103494000-103500200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:103495600-103503600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:103497200-103499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links