Variant report

Variant	rs10975977
Chromosome Location	chr9:7018445-7018446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10429452	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1093708	0.82[JPT][hapmap]
rs1093709	0.82[ASN][1000 genomes]
rs10975958	0.82[ASN][1000 genomes]
rs10975979	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10975982	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10975983	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10976002	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10976003	0.82[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10976004	0.82[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10976011	0.82[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10976016	0.83[EUR][1000 genomes]
rs12002543	0.82[CEU][hapmap]
rs12235561	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12236257	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1323402	0.82[CEU][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407859	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1575451	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1578326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16925141	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16925271	0.81[TSI][hapmap]
rs16925300	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1814048	0.81[JPT][hapmap]
rs2297963	0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2792240	0.81[JPT][hapmap]
rs2792241	0.82[JPT][hapmap]
rs2792242	0.80[JPT][hapmap]
rs2890734	0.82[CEU][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2890735	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3931591	0.80[ASN][1000 genomes]
rs56063552	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60485419	0.81[EUR][1000 genomes]
rs62534416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62534459	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6477148	0.82[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6477151	0.83[EUR][1000 genomes]
rs7021973	0.82[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7024887	0.83[EUR][1000 genomes]
rs7026804	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7031605	0.82[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7032864	0.83[EUR][1000 genomes]
rs7036253	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs7038205	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs72703338	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72703343	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73401806	0.89[ASN][1000 genomes]
rs7848775	0.81[EUR][1000 genomes]
rs7857570	0.81[TSI][hapmap]
rs8181057	0.82[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8181075	1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818881	0.85[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs818890	0.82[JPT][hapmap]
rs818891	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs818893	0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs818897	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
3	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
5	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892187	chr9:6974101-7035727	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv949711	chr9:6994399-7045058	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv892188	chr9:6999846-7026860	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv613257	chr9:7015330-7037370	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:6985600-7019200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:7007800-7019000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr9:7008000-7018800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr9:7008000-7018800	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:7008800-7024200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:7009000-7019000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:7009000-7019800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:7009000-7021600	Weak transcription	HMEC	breast
11	chr9:7009000-7026200	Weak transcription	A549	lung
12	chr9:7009000-7027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr9:7009000-7027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:7009000-7027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:7009000-7028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:7009000-7030400	Weak transcription	NHEK	skin
17	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
19	chr9:7009000-7055200	Weak transcription	K562	blood
20	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
21	chr9:7009000-7076600	Weak transcription	HSMM	muscle
22	chr9:7009200-7077600	Weak transcription	Osteobl	bone
23	chr9:7009400-7019200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:7009400-7029600	Weak transcription	Hela-S3	cervix
25	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
26	chr9:7009600-7020400	Strong transcription	Primary B cells from cord blood	blood
27	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
28	chr9:7010400-7020600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr9:7011000-7021000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:7011200-7019600	Strong transcription	Liver	Liver
31	chr9:7011400-7018800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr9:7011400-7019400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr9:7011400-7020600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:7011600-7019600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:7011600-7019800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr9:7011800-7018800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:7011800-7018800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr9:7012200-7018800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:7012200-7027400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:7012200-7027400	Weak transcription	Brain Anterior Caudate	brain
42	chr9:7012200-7027400	Weak transcription	Right Ventricle	heart
43	chr9:7012200-7027400	Weak transcription	Spleen	Spleen
44	chr9:7012200-7027600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:7012200-7046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
48	chr9:7012400-7018600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:7012400-7018800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:7012400-7018800	Strong transcription	Fetal Thymus	thymus

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