Variant report

Variant	rs11173096
Chromosome Location	chr12:59992825-59992826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747849	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783990	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877316	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1391129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs187991	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2132874	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2365663	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2671853	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2671855	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs402342	0.81[ASW][hapmap]
rs4760290	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11173096	NXPH4	cis	parietal	SCAN
rs11173096	STAT6	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59991000-60005000	Weak transcription	Lung	lung
2	chr12:59991200-60004600	Weak transcription	Ovary	ovary
3	chr12:59991400-59993400	Weak transcription	Right Ventricle	heart
4	chr12:59991400-59994000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:59991400-59994800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:59991400-59994800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr12:59991400-59995400	Weak transcription	Psoas Muscle	Psoas
8	chr12:59991400-59998800	Weak transcription	Left Ventricle	heart
9	chr12:59991400-60004600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:59991400-60004600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:59991400-60004600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:59991400-60005000	Weak transcription	Pancreas	Pancrea
13	chr12:59991400-60009400	Weak transcription	Gastric	stomach
14	chr12:59991600-59994400	Enhancers	Adipose Nuclei	Adipose
15	chr12:59991600-59999000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:59991600-60003600	Weak transcription	Fetal Thymus	thymus
17	chr12:59991600-60004400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:59991600-60004600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:59991600-60004600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:59991600-60004600	Weak transcription	Brain Anterior Caudate	brain
21	chr12:59991600-60004800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:59991600-60005000	Weak transcription	Thymus	Thymus
23	chr12:59991600-60009400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:59991800-59993400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:59991800-59994200	Genic enhancers	Primary T cells from cord blood	blood
26	chr12:59991800-59995600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:59991800-60004800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:59992000-59994400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:59992000-59994600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:59992000-59994800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:59992000-59995400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:59992000-59995800	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:59992000-60004400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:59992000-60004600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:59992200-59993200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:59992200-59994000	Enhancers	NHLF	lung
37	chr12:59992200-59994600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:59992200-59994600	Enhancers	NHDF-Ad	bronchial
39	chr12:59992200-59996400	Weak transcription	Fetal Brain Male	brain
40	chr12:59992200-59997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:59992200-60004600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:59992400-59994200	Strong transcription	Primary B cells from cord blood	blood
43	chr12:59992400-60004600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr12:59992600-59993000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:59992600-59993000	Flanking Active TSS	Fetal Heart	heart
46	chr12:59992600-59993200	Weak transcription	Brain Angular Gyrus	brain
47	chr12:59992600-59999000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:59992600-60013400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:59992800-59993000	Enhancers	Brain Cingulate Gyrus	brain
50	chr12:59992800-59993000	Enhancers	Small Intestine	intestine

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