Variant report

Variant	rs17100509
Chromosome Location	chr1:77852997-77852998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11162326	0.86[JPT][hapmap]
rs11162329	0.88[ASN][1000 genomes]
rs11162335	0.94[ASN][1000 genomes]
rs11584919	1.00[YRI][hapmap]
rs11585455	0.92[JPT][hapmap]
rs11590456	1.00[YRI][hapmap]
rs12043793	0.88[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]
rs17100513	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];0.85[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];0.85[EUR][1000 genomes]
rs2815307	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4949800	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6603943	0.97[ASN][1000 genomes]
rs6673059	0.86[ASN][1000 genomes]
rs6704312	0.85[EUR][1000 genomes]
rs7546116	0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]

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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77839000-77854000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:77845000-77853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:77845200-77853400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:77845200-77860000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:77846400-77859200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:77846600-77853600	Weak transcription	NHLF	lung
9	chr1:77847400-77860200	Weak transcription	HSMM	muscle
10	chr1:77848400-77859400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:77851800-77854800	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:77851800-77854800	Enhancers	Brain Substantia Nigra	brain
13	chr1:77852000-77853400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:77852000-77854800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:77852000-77854800	Enhancers	Brain Anterior Caudate	brain
16	chr1:77852000-77855000	Enhancers	Brain Angular Gyrus	brain
17	chr1:77852000-77855000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr1:77852200-77854400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:77852200-77854600	Weak transcription	Aorta	Aorta
20	chr1:77852400-77853400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:77852400-77855000	Enhancers	Brain Hippocampus Middle	brain
22	chr1:77852600-77853600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:77852600-77853600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:77852800-77853000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:77852800-77853000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:77852800-77853000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:77852800-77853800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:77852800-77855000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:77852800-77855000	Genic enhancers	NHDF-Ad	bronchial

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