Variant report

Variant	rs16908076
Chromosome Location	chr12:12595999-12596000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12590405..12593794-chr12:12593958..12596387,3	MCF-7	breast:
2	chr12:12593955..12596511-chr12:12738215..12739887,2	MCF-7	breast:
3	chr12:12594582..12598614-chr12:12600481..12604032,6	MCF-7	breast:
4	chr12:12584022..12586208-chr12:12592875..12596434,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10505765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10505767	0.82[EUR][1000 genomes]
rs10772566	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10772567	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10845542	0.87[ASN][1000 genomes]
rs10845544	0.87[ASN][1000 genomes]
rs11054894	0.80[ASN][1000 genomes]
rs11054963	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11609375	0.82[CHD][hapmap]
rs11829916	0.87[ASN][1000 genomes]
rs1544682	0.87[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];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16908050	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16908059	1.00[CEU][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908062	1.00[CEU][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908101	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];0.87[ASN][1000 genomes]
rs2193269	0.83[ASN][1000 genomes]
rs2193270	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs2287204	0.85[EUR][1000 genomes]
rs2287205	0.85[EUR][1000 genomes]
rs28853875	0.83[ASN][1000 genomes]
rs3088226	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3751262	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs3803098	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs4633541	0.81[EUR][1000 genomes]
rs4763830	0.82[CHD][hapmap]
rs56089442	0.84[ASN][1000 genomes]
rs56701819	0.89[ASN][1000 genomes]
rs56796062	0.83[ASN][1000 genomes]
rs56915387	0.90[ASN][1000 genomes]
rs57348917	0.80[ASN][1000 genomes]
rs60253266	0.85[ASN][1000 genomes]
rs61543155	0.88[ASN][1000 genomes]
rs7132813	1.00[AFR][1000 genomes]
rs7135655	0.87[CHB][hapmap]
rs7300150	0.82[ASN][1000 genomes]
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];0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7963695	1.00[CEU][hapmap]
rs7967111	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs9645752	0.83[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16908076	TAS2R7	cis	cerebellum	SCAN
rs16908076	GPRC5D	cis	parietal	SCAN
rs16908076	KLRA1	cis	parietal	SCAN
rs16908076	LOH12CR1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12582600-12599400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr12:12582800-12596400	Weak transcription	Spleen	Spleen
3	chr12:12584000-12598600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:12587200-12596400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:12587200-12596400	Weak transcription	Gastric	stomach
6	chr12:12587400-12600200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:12587400-12600200	Weak transcription	Ovary	ovary
8	chr12:12588600-12599400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:12589800-12607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:12590000-12599400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:12590400-12599200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:12590400-12601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:12590600-12599600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
15	chr12:12590800-12599600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr12:12591800-12596800	Enhancers	NHEK	skin
17	chr12:12592000-12596200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:12592000-12596600	Enhancers	HepG2	liver
19	chr12:12592000-12596800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:12592000-12597000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:12592000-12598400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr12:12592200-12597000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:12592200-12600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:12592200-12602200	Enhancers	Fetal Thymus	thymus
25	chr12:12592400-12597600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:12592600-12598200	Enhancers	Stomach Mucosa	stomach
27	chr12:12592800-12598200	Enhancers	Fetal Lung	lung
28	chr12:12593000-12596800	Enhancers	Primary T cells from cord blood	blood
29	chr12:12593000-12597000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:12593200-12596000	Enhancers	Small Intestine	intestine
31	chr12:12593200-12596200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:12593200-12597600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:12593600-12596800	Enhancers	Fetal Heart	heart
34	chr12:12593800-12596000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:12593800-12596800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr12:12593800-12597400	Enhancers	Pancreas	Pancrea
37	chr12:12594000-12596200	Enhancers	K562	blood
38	chr12:12594000-12596400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr12:12594000-12596800	Enhancers	HMEC	breast
40	chr12:12594000-12597000	Enhancers	Brain Anterior Caudate	brain
41	chr12:12594000-12597000	Enhancers	Psoas Muscle	Psoas
42	chr12:12594000-12597000	Enhancers	Right Ventricle	heart
43	chr12:12594000-12597400	Enhancers	Brain Substantia Nigra	brain
44	chr12:12594000-12597400	Enhancers	Left Ventricle	heart
45	chr12:12594000-12597600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr12:12594000-12599200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr12:12594200-12596400	Enhancers	Hela-S3	cervix
48	chr12:12594200-12596600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:12594200-12596800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:12594200-12596800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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