Variant report

Variant	rs7973930
Chromosome Location	chr12:12020170-12020171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10772510	0.91[GIH][hapmap]
rs2239171	0.88[MEX][hapmap]
rs2239172	0.83[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs2739091	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832331	chr12:11925095-12114451	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv516796	chr12:12013985-12027745	Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7973930	PRB3	cis	cerebellum	SCAN
rs7973930	ARHGDIB	cis	cerebellum	SCAN
rs7973930	ZNF705A	cis	parietal	SCAN
rs7973930	CLEC2A	cis	parietal	SCAN
rs7973930	TAS2R20	cis	parietal	SCAN
rs7973930	DUSP16	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11980800-12022600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:11987600-12038000	Weak transcription	Hela-S3	cervix
3	chr12:11989400-12023000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:11996400-12022600	Weak transcription	HSMM	muscle
5	chr12:12005000-12022400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:12009400-12030800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:12014400-12020600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:12014600-12030600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:12014600-12030800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:12015000-12022200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:12015400-12022200	Weak transcription	Esophagus	oesophagus
12	chr12:12016600-12022600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:12016800-12021800	Weak transcription	Lung	lung
14	chr12:12017000-12020800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:12017000-12022200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:12017000-12022200	Weak transcription	Gastric	stomach
17	chr12:12017200-12022200	Weak transcription	Pancreas	Pancrea
18	chr12:12017200-12022400	Weak transcription	Ovary	ovary
19	chr12:12017200-12022600	Weak transcription	Placenta	Placenta
20	chr12:12017200-12022600	Weak transcription	NHLF	lung
21	chr12:12017200-12030600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:12017200-12030800	Weak transcription	NHDF-Ad	bronchial
23	chr12:12017400-12022200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:12017800-12020200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:12018000-12022200	Weak transcription	Spleen	Spleen
26	chr12:12018000-12028400	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:12018800-12027200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:12019000-12020200	ZNF genes & repeats	A549	lung
29	chr12:12019000-12026400	Strong transcription	Fetal Thymus	thymus
30	chr12:12019200-12020200	ZNF genes & repeats	Fetal Lung	lung
31	chr12:12019200-12020200	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr12:12019200-12021200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:12019400-12020600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:12019400-12021800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:12019400-12022400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:12019400-12027000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:12019600-12020600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:12019600-12020800	Weak transcription	Aorta	Aorta
39	chr12:12019600-12020800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:12019600-12021200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:12019600-12021800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:12019600-12022000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:12019600-12022200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:12019600-12022200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:12019600-12022200	Weak transcription	Colonic Mucosa	Colon
46	chr12:12019600-12022200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:12019600-12022200	Weak transcription	Osteobl	bone
48	chr12:12019600-12022400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:12019600-12022600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:12019600-12022600	Weak transcription	Brain Substantia Nigra	brain

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