Variant report

Variant	rs1539670
Chromosome Location	chr9:96000622-96000623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10122466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512233	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs16909000	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs16909005	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16909016	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16936752	1.00[CEU][hapmap]
rs1891971	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891972	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891973	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1936403	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1970622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744197	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744202	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4744205	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55692827	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55706397	0.92[AMR][1000 genomes]
rs55795421	0.95[ASN][1000 genomes]
rs6479467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7029968	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743431	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72743433	0.92[AMR][1000 genomes]
rs72743435	0.92[AMR][1000 genomes]
rs72743442	0.95[ASN][1000 genomes]
rs72743443	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72743444	0.87[ASN][1000 genomes]
rs72743445	0.87[ASN][1000 genomes]
rs7859604	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7859628	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7871272	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
5	chr9:95993600-96005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:95993800-96001800	Weak transcription	Spleen	Spleen
7	chr9:95994000-96001000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:95996200-96001200	Genic enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:95996400-96004400	Strong transcription	Fetal Brain Female	brain
12	chr9:95996400-96011200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr9:95997000-96001800	Strong transcription	HepG2	liver
14	chr9:95997000-96012400	Weak transcription	Fetal Kidney	kidney
15	chr9:95997600-96002000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:95997600-96007000	Weak transcription	Psoas Muscle	Psoas
17	chr9:95997600-96012400	Weak transcription	Fetal Brain Male	brain
18	chr9:95997800-96002400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:95998200-96002000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:95998200-96003000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:95998200-96005800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:95998200-96007200	Weak transcription	Brain Angular Gyrus	brain
23	chr9:95998400-96002200	Weak transcription	Brain Anterior Caudate	brain
24	chr9:95998400-96006400	Strong transcription	Fetal Intestine Large	intestine
25	chr9:95998400-96007000	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:95998400-96007000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:95998800-96000800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr9:95998800-96006600	Strong transcription	Fetal Intestine Small	intestine
29	chr9:95999000-96003000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:95999200-96002000	Weak transcription	Left Ventricle	heart
31	chr9:95999200-96002600	Strong transcription	Colonic Mucosa	Colon
32	chr9:95999200-96006400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:95999200-96006800	Weak transcription	Stomach Mucosa	stomach
34	chr9:95999400-96001800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:95999800-96001400	Strong transcription	Colon Smooth Muscle	Colon
36	chr9:95999800-96001600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:95999800-96003200	Weak transcription	Fetal Heart	heart
38	chr9:96000000-96002600	Strong transcription	Fetal Muscle Leg	muscle
39	chr9:96000200-96000800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:96000200-96002200	Genic enhancers	Rectal Mucosa Donor 29	rectum
41	chr9:96000200-96002400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr9:96000200-96002400	Strong transcription	Right Ventricle	heart
43	chr9:96000400-96000800	Genic enhancers	Placenta	Placenta
44	chr9:96000400-96001200	Strong transcription	Pancreas	Pancrea
45	chr9:96000400-96001600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr9:96000400-96002400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr9:96000400-96002600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:96000400-96004200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:96000600-96001000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:96000600-96001000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links