Variant report

Variant	rs7990472
Chromosome Location	chr13:49563833-49563834
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	chr13:49563178..49565199-chr13:49566852..49568731,2	K562	blood:
2	chr13:49554312..49556317-chr13:49562334..49565268,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1159972	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11617719	0.87[EUR][1000 genomes]
rs11620305	0.86[EUR][1000 genomes]
rs12429554	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17477129	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs35468616	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61950726	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61950727	0.91[EUR][1000 genomes]
rs61950730	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034	chr13:49526761-49572727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv900067	chr13:49552271-49594818	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv900068	chr13:49559790-49605774	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7990472	KCNRG	cis	cerebellum	SCAN
rs7990472	CAB39L	cis	cerebellum	SCAN
rs7990472	SNORA31	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49551800-49569400	Weak transcription	Psoas Muscle	Psoas
3	chr13:49552200-49570400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:49553400-49564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:49553600-49596200	Weak transcription	Ovary	ovary
6	chr13:49554000-49565200	Weak transcription	Osteobl	bone
7	chr13:49554200-49564600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:49554200-49565400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:49554200-49573000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:49554200-49573200	Weak transcription	NHDF-Ad	bronchial
11	chr13:49554400-49567400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr13:49554400-49568600	Weak transcription	Placenta	Placenta
13	chr13:49554600-49564600	Weak transcription	Fetal Intestine Small	intestine
14	chr13:49554600-49565600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr13:49554600-49568600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr13:49555000-49564200	Weak transcription	Primary T cells from cord blood	blood
17	chr13:49555000-49569200	Weak transcription	HMEC	breast
18	chr13:49555000-49573000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:49555000-49581600	Weak transcription	Left Ventricle	heart
20	chr13:49555200-49564800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr13:49555600-49564800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr13:49557000-49579800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr13:49557000-49626800	Weak transcription	Right Ventricle	heart
24	chr13:49557200-49573200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:49557800-49567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:49558000-49565200	Weak transcription	Stomach Mucosa	stomach
27	chr13:49558200-49564800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:49560000-49587600	Weak transcription	Fetal Kidney	kidney
29	chr13:49560200-49564800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:49560200-49572000	Weak transcription	Colon Smooth Muscle	Colon
31	chr13:49560200-49578000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:49560200-49581000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:49560600-49564800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr13:49560800-49587200	Weak transcription	Small Intestine	intestine
35	chr13:49562000-49572800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr13:49562400-49573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:49563200-49566200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:49563400-49567000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr13:49563600-49564000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr13:49563800-49573000	Weak transcription	Hela-S3	cervix
41	chr13:49563800-49583400	Weak transcription	Fetal Heart	heart

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