Variant report

Variant	rs6545971
Chromosome Location	chr2:63074986-63074987
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63073137..63075941-chr2:63076155..63077726,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153716	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1022110	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11682530	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11688816	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11893131	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12328837	0.93[JPT][hapmap]
rs12713467	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12713468	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12713469	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs12989754	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12994674	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13013218	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13398408	0.87[YRI][hapmap]
rs13418889	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1420018	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1468748	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.86[JPT][hapmap]
rs1534420	0.86[JPT][hapmap]
rs1553832	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17027429	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1828398	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1872789	0.81[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs189671	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1906198	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs2058566	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058567	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2080227	0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2136737	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.86[JPT][hapmap]
rs2215870	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421816	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2430386	0.84[AFR][1000 genomes]
rs2430388	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2539978	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2539980	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2539981	0.86[AFR][1000 genomes]
rs2539982	0.86[AFR][1000 genomes]
rs2539985	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2539987	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs2539990	0.82[AFR][1000 genomes]
rs2710637	0.91[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs2710638	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2710639	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2710640	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710642	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710651	0.82[AFR][1000 genomes]
rs34104251	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs360797	0.86[CEU][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap]
rs360799	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs360800	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs360801	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs360804	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs360807	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs3927201	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4461246	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671050	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs4671051	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4671450	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6545969	0.93[JPT][hapmap]
rs6545972	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6545973	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6705798	0.90[CEU][hapmap]
rs6739804	0.90[CEU][hapmap];0.89[CHB][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7562149	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7562734	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567923	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7571916	0.88[EUR][1000 genomes]
rs7573756	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9678329	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9789661	0.84[EUR][1000 genomes]
rs9973612	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
2	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
4	chr2:63040600-63082000	Weak transcription	Lung	lung
5	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
9	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:63055000-63082000	Weak transcription	Esophagus	oesophagus
12	chr2:63056400-63081800	Weak transcription	NHLF	lung
13	chr2:63060800-63081000	Weak transcription	Left Ventricle	heart
14	chr2:63060800-63081800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:63061000-63080400	Weak transcription	Aorta	Aorta
16	chr2:63061200-63080800	Weak transcription	Psoas Muscle	Psoas
17	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:63061400-63080400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:63061600-63082000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:63061800-63080800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:63062000-63076400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:63062000-63080600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:63062000-63081200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:63062000-63082400	Weak transcription	HMEC	breast
26	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:63062200-63076400	Weak transcription	Osteobl	bone
28	chr2:63062200-63080600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:63063000-63081800	Weak transcription	Fetal Stomach	stomach
30	chr2:63063200-63075800	Weak transcription	Fetal Intestine Large	intestine
31	chr2:63071200-63097200	Strong transcription	HepG2	liver
32	chr2:63072000-63086200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:63072200-63082800	Weak transcription	Primary T cells from cord blood	blood
34	chr2:63072200-63083400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:63072600-63101800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:63072800-63080600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:63072800-63083600	Weak transcription	Right Ventricle	heart
38	chr2:63073400-63075600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:63073400-63076200	Weak transcription	NH-A	brain
40	chr2:63073400-63077800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:63073400-63080400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:63073400-63080400	Weak transcription	Ovary	ovary
43	chr2:63073400-63080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:63073400-63080800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:63073400-63083800	Weak transcription	Fetal Heart	heart
46	chr2:63073400-63093000	Weak transcription	Primary B cells from cord blood	blood
47	chr2:63073600-63078000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:63073600-63080200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:63073600-63080400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:63073600-63080400	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links