Variant report

Variant	rs2645104
Chromosome Location	chr6:37979956-37979957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37786027..37788545-chr6:37979008..37980609,2	MCF-7	breast:
2	chr6:37974723..37976308-chr6:37979935..37981504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11759458	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11964613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[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];0.95[AMR][1000 genomes]
rs11964671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs11968604	0.91[AMR][1000 genomes]
rs11970017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes]
rs11970145	0.95[AMR][1000 genomes]
rs13198459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13203867	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13205214	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs13207526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13210087	0.95[ASN][1000 genomes]
rs13210967	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs13211881	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13217630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13218158	0.95[AMR][1000 genomes]
rs13219500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16890185	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs16890194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs16890301	0.88[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs16890365	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2395689	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs2453882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2645096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes]
rs2645098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2645115	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645118	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645121	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645123	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2842498	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2842506	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2842511	0.89[CEU][hapmap]
rs2842513	0.83[AMR][1000 genomes]
rs2842514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2842516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2842524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34011349	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34038972	0.80[EUR][1000 genomes]
rs34054102	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34123707	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34406273	0.80[EUR][1000 genomes]
rs34611895	0.95[AMR][1000 genomes]
rs34745343	0.95[AMR][1000 genomes]
rs34754573	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35202194	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35248825	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35330991	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35597126	0.80[EUR][1000 genomes]
rs35609407	0.95[AMR][1000 genomes]
rs35953900	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4394213	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs55943813	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56391784	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6458037	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6908106	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6908761	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6910837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6911481	0.86[AMR][1000 genomes]
rs6912250	0.95[AMR][1000 genomes]
rs6916057	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6916535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6917208	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs6918802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6919884	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6923132	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6923254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6923665	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6925563	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6933547	1.00[YRI][hapmap]
rs6940491	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71569395	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs71569399	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71569402	0.87[EUR][1000 genomes]
rs7740636	0.80[EUR][1000 genomes]
rs7742379	0.95[AMR][1000 genomes]
rs7747538	0.87[AFR][1000 genomes]
rs7757560	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7760770	0.91[AMR][1000 genomes]
rs7766767	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7776025	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9296236	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv34450	chr6:37963308-38007241	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37960800-37982400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:37963000-37984800	Weak transcription	Right Atrium	heart
3	chr6:37963000-37995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:37965600-37982200	Weak transcription	Psoas Muscle	Psoas
5	chr6:37969200-37987800	Weak transcription	Fetal Kidney	kidney
6	chr6:37970800-37984200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:37972400-37983800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:37974800-37984600	Weak transcription	Placenta	Placenta
9	chr6:37976600-37983000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:37976600-37988400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:37976800-37983200	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:37976800-37987800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:37977400-37982600	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:37978200-37987600	Weak transcription	Pancreas	Pancrea
15	chr6:37978600-37983000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:37979200-37984400	Weak transcription	Primary B cells from cord blood	blood
17	chr6:37979400-37989000	Weak transcription	Primary T cells from cord blood	blood
18	chr6:37979800-37980000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:37979800-37980000	ZNF genes & repeats	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links