Variant report

Variant	rs11175172
Chromosome Location	chr12:64183598-64183599
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64173978..64177817-chr12:64182120..64184728,4	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11175174	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301671	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1876465	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1983148	0.89[LWK][hapmap];0.88[YRI][hapmap]
rs2279964	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791156	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581507	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7304120	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs73313417	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949955	0.87[ASW][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs949956	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv899171	chr12:63916682-64202233	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv430514	chr12:63939733-64183598	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3485882	chr12:64178755-64196017	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3485883	chr12:64178755-64196017	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3488108	chr12:64178778-64195988	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3488119	chr12:64178778-64195988	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11175172	SLC16A7	cis	cerebellum	SCAN
rs11175172	TBK1	cis	cerebellum	SCAN
rs11175172	SRGAP1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64174400-64184000	Weak transcription	Esophagus	oesophagus
2	chr12:64174400-64184000	Weak transcription	Lung	lung
3	chr12:64174400-64189200	Weak transcription	Pancreas	Pancrea
4	chr12:64174400-64200200	Weak transcription	Spleen	Spleen
5	chr12:64174400-64201800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:64174400-64203400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:64174400-64204400	Weak transcription	Small Intestine	intestine
8	chr12:64174400-64204800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:64174600-64183800	Weak transcription	Psoas Muscle	Psoas
10	chr12:64174600-64186200	Weak transcription	Aorta	Aorta
11	chr12:64174600-64187800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:64174600-64199400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:64174600-64200200	Weak transcription	HSMMtube	muscle
14	chr12:64174600-64200600	Weak transcription	Thymus	Thymus
15	chr12:64174600-64201000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:64174600-64204400	Weak transcription	Colonic Mucosa	Colon
17	chr12:64174800-64199200	Weak transcription	Stomach Mucosa	stomach
18	chr12:64174800-64208000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:64174800-64208000	Weak transcription	Fetal Brain Male	brain
20	chr12:64174800-64208600	Weak transcription	Fetal Brain Female	brain
21	chr12:64175000-64183800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:64175000-64184000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:64175000-64184600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:64175000-64186000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:64175000-64186000	Weak transcription	Brain Germinal Matrix	brain
26	chr12:64175000-64189000	Weak transcription	Fetal Intestine Small	intestine
27	chr12:64175000-64200200	Weak transcription	Brain Anterior Caudate	brain
28	chr12:64175200-64184800	Strong transcription	Placenta	Placenta
29	chr12:64175200-64185600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:64175200-64199400	Weak transcription	NHLF	lung
31	chr12:64175200-64202400	Weak transcription	Fetal Heart	heart
32	chr12:64175200-64205200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:64175400-64189400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:64175400-64200800	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:64175400-64201800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:64175400-64202600	Weak transcription	Hela-S3	cervix
37	chr12:64175400-64202800	Weak transcription	HUVEC	blood vessel
38	chr12:64175400-64204400	Weak transcription	Brain Angular Gyrus	brain
39	chr12:64175600-64183600	Weak transcription	Fetal Kidney	kidney
40	chr12:64175600-64186400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:64175600-64189800	Weak transcription	HepG2	liver
42	chr12:64175600-64208000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:64176200-64185200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:64176200-64186600	Strong transcription	Dnd41	blood
45	chr12:64176800-64183800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:64177600-64186200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:64178000-64209800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:64178200-64183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:64178400-64188600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:64178400-64204000	Weak transcription	HMEC	breast

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