Variant report

Variant	rs2615999
Chromosome Location	chr1:103346219-103346220
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 181 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs1012282	1.00[JPT][hapmap]
rs1012283	0.85[ASN][1000 genomes]
rs1020918	0.87[AFR][1000 genomes]
rs1031820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10782921	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874665	1.00[JPT][hapmap]
rs10874668	1.00[JPT][hapmap]
rs10874672	0.80[ASN][1000 genomes]
rs11164648	1.00[JPT][hapmap]
rs11164649	1.00[JPT][hapmap]
rs11164653	1.00[JPT][hapmap]
rs11164658	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11809524	1.00[JPT][hapmap]
rs11811018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12025848	1.00[JPT][hapmap]
rs12047268	1.00[JPT][hapmap]
rs12118365	1.00[JPT][hapmap]
rs12119459	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12123031	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12127590	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12136338	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12136748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12139120	1.00[JPT][hapmap]
rs12142524	0.85[ASN][1000 genomes]
rs12143676	0.85[ASN][1000 genomes]
rs1241162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1241164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1241165	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1241166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1241172	0.81[EUR][1000 genomes]
rs1241173	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1241181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1241182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1241183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1241184	0.81[YRI][hapmap]
rs1241190	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1241197	0.80[AMR][1000 genomes]
rs1241205	0.88[AFR][1000 genomes]
rs1241207	0.88[AFR][1000 genomes]
rs1241208	0.88[AFR][1000 genomes]
rs12723167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12723922	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12724152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12726009	0.82[CHB][hapmap]
rs12726958	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12728397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12728737	0.80[ASN][1000 genomes]
rs12729449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12729602	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12731575	1.00[ASN][1000 genomes]
rs12731622	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12731843	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12733933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12736509	0.92[ASN][1000 genomes]
rs12738133	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12740462	0.85[ASN][1000 genomes]
rs12742130	0.80[ASN][1000 genomes]
rs12742440	0.80[ASN][1000 genomes]
rs12743150	0.80[ASN][1000 genomes]
rs12743365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12744290	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12744488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12748384	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12749981	0.83[ASN][1000 genomes]
rs12750179	0.85[ASN][1000 genomes]
rs12750377	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12753580	0.80[ASN][1000 genomes]
rs12753781	0.80[ASN][1000 genomes]
rs12756627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1337174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1337175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1337186	1.00[JPT][hapmap]
rs1463034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1463035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1463037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1463038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1463039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1538041	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1564143	1.00[JPT][hapmap]
rs1591636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1591637	1.00[JPT][hapmap]
rs1621055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1622838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676495	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1676498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676502	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1676508	0.85[AFR][1000 genomes]
rs17447925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17506286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17507967	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1763343	0.87[AFR][1000 genomes]
rs1763344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1763345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1763346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1763349	0.87[AFR][1000 genomes]
rs1763350	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1870958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1903787	1.00[JPT][hapmap]
rs1932333	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1932336	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2050601	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2061704	1.00[JPT][hapmap]
rs2065922	1.00[JPT][hapmap]
rs2252146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2254082	1.00[JPT][hapmap]
rs2615977	1.00[JPT][hapmap]
rs2615987	1.00[JPT][hapmap]
rs2622840	0.80[ASN][1000 genomes]
rs2622848	1.00[JPT][hapmap]
rs2622870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622877	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2783570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2786120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2786121	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2786122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2786125	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2929163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3102053	1.00[JPT][hapmap]
rs34090601	0.85[ASN][1000 genomes]
rs34277983	0.85[ASN][1000 genomes]
rs34413966	0.85[ASN][1000 genomes]
rs34542642	0.85[ASN][1000 genomes]
rs34882475	0.85[ASN][1000 genomes]
rs35150936	0.80[ASN][1000 genomes]
rs35486863	0.92[ASN][1000 genomes]
rs35498106	0.85[ASN][1000 genomes]
rs35613209	0.85[ASN][1000 genomes]
rs35839974	0.90[ASN][1000 genomes]
rs3767272	1.00[CHB][hapmap]
rs3850459	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4353117	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4478834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4907983	0.87[AFR][1000 genomes]
rs4908280	1.00[JPT][hapmap]
rs66473612	0.85[ASN][1000 genomes]
rs66531224	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs66626223	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6663034	1.00[JPT][hapmap]
rs6670486	1.00[JPT][hapmap]
rs6672647	1.00[JPT][hapmap]
rs6695665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67016898	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs67621984	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs68109992	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71512566	0.85[ASN][1000 genomes]
rs71664950	0.85[ASN][1000 genomes]
rs71664951	0.85[ASN][1000 genomes]
rs71664952	0.80[ASN][1000 genomes]
rs71664954	0.80[ASN][1000 genomes]
rs71664955	0.80[ASN][1000 genomes]
rs7517682	1.00[JPT][hapmap]
rs7532572	1.00[JPT][hapmap]
rs7544130	1.00[JPT][hapmap]
rs945748	1.00[JPT][hapmap]
rs969272	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830882	chr1:103192683-103355802	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	nsv546928	chr1:103331349-103371652	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv871829	chr1:103336601-103367095	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	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
6	nsv871808	chr1:103339272-103367095	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv870725	chr1:103339272-103371032	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv870821	chr1:103339272-103379918	Active TSS ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv871809	chr1:103339272-103459537	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv871732	chr1:103339272-103466917	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	nsv546929	chr1:103342392-103371652	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
13	nsv462728	chr1:103342392-103455217	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv546930	chr1:103342392-103455217	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103334000-103349800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:103335400-103350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:103338400-103369400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:103338800-103357200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:103339200-103349800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:103340800-103350000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:103341400-103349800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:103341600-103352000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:103342400-103349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:103343400-103352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:103343400-103355800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:103343400-103356200	Weak transcription	Fetal Heart	heart
13	chr1:103343400-103366000	Weak transcription	Fetal Brain Female	brain
14	chr1:103344400-103349800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:103345000-103346400	Enhancers	HMEC	breast
16	chr1:103345000-103348000	Enhancers	HUVEC	blood vessel
17	chr1:103345400-103347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:103345600-103346400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:103345600-103346400	Enhancers	A549	lung
20	chr1:103345600-103346400	Enhancers	Osteobl	bone
21	chr1:103345600-103347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:103345600-103347600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:103345600-103350600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:103345600-103385600	Weak transcription	HSMMtube	muscle
25	chr1:103345800-103346400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:103345800-103357200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:103346000-103347200	Weak transcription	HSMM	muscle
28	chr1:103346000-103348000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:103346000-103350200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:103346200-103347000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:103346200-103347200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:103346200-103357400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:103346200-103357400	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links