Variant report

Variant	rs17100513
Chromosome Location	chr1:77864321-77864322
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	chr1:77863743..77865980-chr1:77869588..77871346,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10873935	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11162326	0.86[JPT][hapmap]
rs11162329	0.82[ASN][1000 genomes]
rs11162335	1.00[ASN][1000 genomes]
rs11584919	1.00[YRI][hapmap]
rs11585455	0.92[JPT][hapmap]
rs11590456	1.00[YRI][hapmap]
rs12043793	0.82[ASN][1000 genomes]
rs12124822	1.00[YRI][hapmap]
rs12125503	1.00[YRI][hapmap]
rs12128049	1.00[YRI][hapmap]
rs12132273	1.00[YRI][hapmap]
rs12135843	1.00[YRI][hapmap]
rs12140227	1.00[YRI][hapmap]
rs12141929	1.00[YRI][hapmap]
rs12565526	0.86[JPT][hapmap]
rs17100509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198511	1.00[ASW][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2602936	1.00[GIH][hapmap];0.92[JPT][hapmap]
rs2602937	0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2815307	1.00[ASW][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4949800	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6603943	0.97[ASN][1000 genomes]
rs6673059	0.91[ASN][1000 genomes]
rs6704312	0.80[EUR][1000 genomes]
rs7546116	0.84[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:77854000-77865200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:77859400-77865600	Enhancers	Brain Anterior Caudate	brain
5	chr1:77859800-77865600	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:77859800-77866200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:77860000-77866200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:77860000-77866600	Enhancers	Brain Hippocampus Middle	brain
9	chr1:77860800-77866000	Enhancers	Brain Angular Gyrus	brain
10	chr1:77861000-77866400	Enhancers	Brain Substantia Nigra	brain
11	chr1:77861200-77865000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:77861200-77865000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:77861400-77865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:77861400-77865200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:77861400-77865600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr1:77861600-77865600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:77861600-77871800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:77862000-77864400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:77862600-77865000	Weak transcription	NHDF-Ad	bronchial
20	chr1:77862800-77865200	Weak transcription	Osteobl	bone
21	chr1:77862800-77865600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:77862800-77866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:77863200-77865000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:77863200-77871800	Weak transcription	Aorta	Aorta
25	chr1:77863600-77864400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:77863600-77866000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:77863800-77864400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:77863800-77864600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:77864000-77865800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:77864000-77867400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:77864200-77864400	Enhancers	Brain Germinal Matrix	brain
32	chr1:77864200-77864600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:77864200-77865200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:77864200-77871200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links