Variant report

Variant	rs7597961
Chromosome Location	chr2:9751478-9751479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:9750992-9751841	A549	lung:	n/a	n/a
2	POLR2A	chr2:9750980-9757087	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:9751388-9751490	HepG2	liver:	n/a	n/a
4	CEBPB	chr2:9751346-9751742	IMR90	lung:	n/a	chr2:9751593-9751604
5	SETDB1	chr2:9751208-9751656	U2OS	brain:	n/a	n/a
6	KAP1	chr2:9751136-9751692	HEK293	kidney:	n/a	n/a
7	POLR2A	chr2:9751454-9751578	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:9717251..9718757-chr2:9750953..9752940,2	MCF-7	breast:
2	chr2:9735520..9737713-chr2:9751112..9753286,2	MCF-7	breast:
3	chr2:9614693..9617599-chr2:9751058..9753194,2	K562	blood:

Variant related genes	Relation type
ENSG00000207086	TF binding region
ENSG00000134330	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11674777	1.00[JPT][hapmap]
rs11888902	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11890807	1.00[JPT][hapmap]
rs11902264	1.00[JPT][hapmap]
rs11902431	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12465158	0.90[EUR][1000 genomes]
rs12470619	0.90[EUR][1000 genomes]
rs12476008	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12692388	1.00[JPT][hapmap]
rs16867062	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16867073	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16867074	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs3791748	1.00[JPT][hapmap]
rs41308184	0.93[EUR][1000 genomes]
rs4669401	0.90[EUR][1000 genomes]
rs62119390	0.90[EUR][1000 genomes]
rs62119425	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62119430	1.00[EUR][1000 genomes]
rs6432018	1.00[JPT][hapmap]
rs6432023	1.00[JPT][hapmap]
rs6432025	1.00[JPT][hapmap]
rs6715408	0.93[EUR][1000 genomes]
rs6734469	1.00[JPT][hapmap]
rs7569485	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7597961	LOC645233///LOC732360///TDG	trans	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9741400-9752600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:9741400-9760000	Weak transcription	Fetal Kidney	kidney
4	chr2:9741800-9752600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:9742000-9753600	Weak transcription	Fetal Lung	lung
6	chr2:9742200-9757000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:9742400-9753400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:9742800-9752400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:9742800-9757800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:9744600-9755200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:9744800-9766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:9746800-9752800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:9747600-9751600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr2:9747800-9760200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:9748000-9757000	Enhancers	Brain Hippocampus Middle	brain
16	chr2:9748600-9753000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:9748600-9755000	Weak transcription	Fetal Stomach	stomach
18	chr2:9748600-9756400	Enhancers	Brain Substantia Nigra	brain
19	chr2:9748600-9765600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:9748600-9766600	Weak transcription	Aorta	Aorta
21	chr2:9748600-9767600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:9748800-9751800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:9748800-9752000	Weak transcription	Right Atrium	heart
24	chr2:9748800-9752200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:9748800-9752200	Weak transcription	Placenta	Placenta
26	chr2:9748800-9752400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:9748800-9752600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:9748800-9752600	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:9748800-9752800	Weak transcription	HMEC	breast
30	chr2:9748800-9753000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:9748800-9753600	Weak transcription	HSMMtube	muscle
32	chr2:9748800-9758800	Weak transcription	Thymus	Thymus
33	chr2:9748800-9761200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:9748800-9763400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:9749000-9751600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:9749000-9751600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:9749000-9751800	Weak transcription	Colonic Mucosa	Colon
38	chr2:9749000-9751800	Weak transcription	Esophagus	oesophagus
39	chr2:9749000-9752000	Weak transcription	Small Intestine	intestine
40	chr2:9749000-9752200	Weak transcription	HSMM	muscle
41	chr2:9749000-9752400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:9749000-9752400	Weak transcription	Fetal Thymus	thymus
43	chr2:9749000-9752800	Weak transcription	Spleen	Spleen
44	chr2:9749000-9753800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:9749000-9753800	Weak transcription	Fetal Brain Female	brain
46	chr2:9749000-9754400	Weak transcription	Fetal Intestine Small	intestine
47	chr2:9749000-9755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:9749000-9756800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:9749000-9757800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:9749000-9764600	Weak transcription	Lung	lung

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