Variant report

Variant	rs16908101
Chromosome Location	chr12:12609988-12609989
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	CEBPB	chr12:12609667-12610019	IMR90	lung:	n/a	n/a
2	MAFK	chr12:12609604-12609989	IMR90	lung:	n/a	chr12:12609785-12609800 chr12:12609790-12609801 chr12:12609785-12609801 chr12:12609790-12609801
3	STAT3	chr12:12609591-12610005	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:12609698-12610105	MCF10A-Er-Src	breast:	n/a	n/a
5	TCF12	chr12:12609391-12610070	SK-N-SH	brain:	n/a	n/a
6	FOS	chr12:12609552-12610005	MCF10A-Er-Src	breast:	n/a	n/a
7	GATA3	chr12:12609434-12610029	SK-N-SH	brain:	n/a	chr12:12609969-12609976 chr12:12609966-12609976 chr12:12609969-12609976 chr12:12609962-12609983 chr12:12609969-12609976 chr12:12609965-12609981

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12509893..12512192-chr12:12607942..12610815,2	MCF-7	breast:
2	chr12:12609394..12612369-chr12:12615599..12621309,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271370	TF binding region
ENSG00000205791	Chromatin interaction
ENSG00000165714	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10505765	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10505767	0.82[EUR][1000 genomes]
rs10772566	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10772567	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10845542	0.84[ASN][1000 genomes]
rs10845544	0.84[ASN][1000 genomes]
rs11054963	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11609375	0.82[CHD][hapmap]
rs11829916	0.85[ASN][1000 genomes]
rs11834080	0.81[CHB][hapmap]
rs1544682	0.84[ASN][1000 genomes]
rs16907990	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16908050	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16908059	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16908062	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16908072	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16908076	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16908146	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908151	0.85[EUR][1000 genomes]
rs16908167	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16908171	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908188	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908204	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908209	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16908214	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16916539	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17312766	0.81[EUR][1000 genomes]
rs17378260	0.81[EUR][1000 genomes]
rs2160586	0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2193269	0.80[ASN][1000 genomes]
rs2193270	0.94[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs2287204	0.85[EUR][1000 genomes]
rs2287205	0.85[EUR][1000 genomes]
rs28853875	0.80[ASN][1000 genomes]
rs3088226	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3751262	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs3803098	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs4633541	0.81[EUR][1000 genomes]
rs4763830	0.82[CHD][hapmap]
rs56089442	0.81[ASN][1000 genomes]
rs56701819	0.86[ASN][1000 genomes]
rs56796062	0.80[ASN][1000 genomes]
rs56915387	0.88[ASN][1000 genomes]
rs60253266	0.82[ASN][1000 genomes]
rs61543155	0.85[ASN][1000 genomes]
rs7132813	1.00[AFR][1000 genomes]
rs7135655	0.82[CHB][hapmap]
rs7309503	0.81[CHD][hapmap]
rs7309982	0.81[CHD][hapmap]
rs7313825	0.82[CHD][hapmap]
rs745632	0.82[EUR][1000 genomes]
rs7486371	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7963695	1.00[CEU][hapmap]
rs7967111	0.84[CHD][hapmap]
rs9645752	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3501463	chr12:12609779-12610326	Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3391765	chr12:12609789-12610324	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3501474	chr12:12609793-12610322	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16908101	LOH12CR1	cis	lymphoblastoid	seeQTL
rs16908101	TAS2R7	cis	cerebellum	SCAN
rs16908101	GPRC5D	cis	parietal	SCAN
rs16908101	KLRA1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:12596000-12620200	Weak transcription	HSMM	muscle
5	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:12597000-12617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:12597400-12618200	Weak transcription	Gastric	stomach
11	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
13	chr12:12600600-12616800	Weak transcription	Fetal Stomach	stomach
14	chr12:12600800-12610200	Weak transcription	Brain Anterior Caudate	brain
15	chr12:12601000-12620200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:12602200-12610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:12602600-12610600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:12602800-12610000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:12603200-12618400	Weak transcription	Esophagus	oesophagus
20	chr12:12603400-12618600	Weak transcription	Pancreas	Pancrea
21	chr12:12603800-12614200	Weak transcription	Aorta	Aorta
22	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
24	chr12:12604600-12613600	Weak transcription	Fetal Intestine Small	intestine
25	chr12:12604600-12618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:12605200-12618400	Weak transcription	Liver	Liver
27	chr12:12605600-12610400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:12607800-12629400	Weak transcription	Fetal Kidney	kidney
29	chr12:12608400-12627200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:12608400-12629600	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:12609000-12611000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:12609000-12611200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr12:12609000-12611400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:12609000-12623400	Weak transcription	A549	lung
35	chr12:12609200-12610000	Enhancers	GM12878-XiMat	blood
36	chr12:12609200-12610200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr12:12609200-12610200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr12:12609200-12610200	Enhancers	HUVEC	blood vessel
39	chr12:12609200-12610400	Enhancers	Fetal Intestine Large	intestine
40	chr12:12609200-12610600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:12609200-12610800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:12609200-12611000	Enhancers	NH-A	brain
43	chr12:12609200-12611200	Enhancers	Brain Hippocampus Middle	brain
44	chr12:12609200-12611400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr12:12609200-12626800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:12609400-12610200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:12609400-12610600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:12609400-12611000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:12609400-12611200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:12609400-12611400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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