Variant report

Variant	rs12596703
Chromosome Location	chr16:12213850-12213851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12213304..12215275-chr16:12226853..12228529,2	MCF-7	breast:
2	chr16:12207504..12209871-chr16:12211621..12214983,3	K562	blood:
3	chr16:12212007..12215167-chr16:12222860..12225449,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048471	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11075049	0.82[JPT][hapmap]
rs11075054	0.99[ASN][1000 genomes]
rs11639701	0.84[ASN][1000 genomes]
rs11642033	0.96[ASN][1000 genomes]
rs11642386	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11646458	0.92[ASN][1000 genomes]
rs11646539	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11646584	0.96[ASN][1000 genomes]
rs11647572	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648228	0.82[ASN][1000 genomes]
rs11648468	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs11648816	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12596549	0.82[ASN][1000 genomes]
rs12599090	0.82[ASN][1000 genomes]
rs12599107	0.92[ASN][1000 genomes]
rs12599793	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12708747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12924889	0.93[ASN][1000 genomes]
rs12926900	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12929519	0.96[ASN][1000 genomes]
rs13333662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13336687	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs16958964	0.90[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2136250	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175020	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs34098770	0.91[ASN][1000 genomes]
rs34147612	0.83[ASN][1000 genomes]
rs34598762	0.83[ASN][1000 genomes]
rs35053871	0.82[ASN][1000 genomes]
rs35293822	0.97[ASN][1000 genomes]
rs35318501	0.80[ASN][1000 genomes]
rs35542345	0.96[ASN][1000 genomes]
rs3851011	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3851012	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3851013	0.94[ASN][1000 genomes]
rs3851014	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3862466	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3893358	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4780411	0.82[ASN][1000 genomes]
rs4781180	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs71385189	0.82[ASN][1000 genomes]
rs7200307	0.82[ASN][1000 genomes]
rs8048589	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs8050180	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs8059989	0.82[ASN][1000 genomes]
rs8063329	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9925009	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs9935284	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9936270	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9939383	0.82[JPT][hapmap]

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	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12596703	SHISA9	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:12189800-12220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr16:12190000-12220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:12190000-12220400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr16:12191200-12223200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr16:12192000-12214600	Weak transcription	Right Atrium	heart
7	chr16:12194000-12215200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:12198200-12227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:12200200-12220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr16:12200600-12215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:12204800-12222000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr16:12207200-12218400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr16:12208000-12221200	Weak transcription	Brain Substantia Nigra	brain
14	chr16:12208200-12228000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr16:12208400-12214200	Weak transcription	Fetal Brain Female	brain
16	chr16:12208400-12218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr16:12208400-12218800	Weak transcription	Brain Anterior Caudate	brain
18	chr16:12208600-12226800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:12211000-12218600	Weak transcription	Thymus	Thymus
20	chr16:12211000-12218600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr16:12211000-12224400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr16:12211000-12227800	Weak transcription	Fetal Intestine Small	intestine
23	chr16:12211200-12214600	Weak transcription	Fetal Kidney	kidney
24	chr16:12211200-12215000	Weak transcription	Spleen	Spleen
25	chr16:12211200-12218400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr16:12211200-12221400	Weak transcription	GM12878-XiMat	blood
27	chr16:12211200-12223200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:12211200-12223400	Weak transcription	Aorta	Aorta
29	chr16:12211200-12224400	Weak transcription	Pancreas	Pancrea
30	chr16:12211200-12226200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:12211600-12218400	Weak transcription	Primary B cells from cord blood	blood
32	chr16:12212400-12214000	Enhancers	Esophagus	oesophagus
33	chr16:12212600-12215000	Enhancers	Ovary	ovary
34	chr16:12212600-12215400	Enhancers	HepG2	liver
35	chr16:12212600-12215600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr16:12212800-12214200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr16:12212800-12214400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:12212800-12214400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr16:12212800-12215000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr16:12212800-12215200	Enhancers	NHDF-Ad	bronchial
41	chr16:12212800-12215400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr16:12213000-12214000	Enhancers	HSMM	muscle
43	chr16:12213000-12215200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:12213000-12215200	Enhancers	Fetal Stomach	stomach
45	chr16:12213000-12215400	Enhancers	Left Ventricle	heart
46	chr16:12213000-12215600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr16:12213000-12215600	Enhancers	Fetal Heart	heart
48	chr16:12213000-12215600	Enhancers	Fetal Muscle Leg	muscle
49	chr16:12213000-12215600	Enhancers	Placenta	Placenta
50	chr16:12213000-12215600	Enhancers	Right Ventricle	heart

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