Variant report

Variant	rs11172147
Chromosome Location	chr12:57696677-57696678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57691946..57694980-chr12:57695463..57699160,3	K562	blood:
2	chr12:57692883..57695255-chr12:57696474..57700036,3	K562	blood:
3	chr12:57683640..57687551-chr12:57695427..57698739,4	K562	blood:
4	chr12:57696649..57699351-chr12:57704431..57706467,2	K562	blood:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1106766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[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]
rs11172134	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11172181	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11609805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11612551	0.83[MEX][hapmap]
rs11613352	1.00[CEU][hapmap];0.82[AFR][1000 genomes]
rs11614506	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs12313306	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12313762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2229357	1.00[JPT][hapmap]
rs3741414	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4760254	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4760278	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs4760355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs540730	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs56205943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7397189	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7484541	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7485577	0.83[MEX][hapmap]
rs7964492	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7971133	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11172147	XRCC6BP1	cis	parietal	SCAN
rs11172147	IL23A	cis	parietal	SCAN
rs11172147	KRT2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57654800-57705400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57662800-57706000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:57670400-57707000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:57670600-57698600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:57670600-57700000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:57671000-57700000	Strong transcription	Liver	Liver
7	chr12:57674400-57697000	Strong transcription	Placenta	Placenta
8	chr12:57674600-57697000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:57674600-57700000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:57674600-57702600	Weak transcription	HUVEC	blood vessel
11	chr12:57674600-57704400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:57674800-57697400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:57674800-57697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:57674800-57700000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:57674800-57701000	Strong transcription	Primary T cells from cord blood	blood
16	chr12:57675000-57698400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:57675000-57699400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:57675000-57700000	Strong transcription	Fetal Thymus	thymus
19	chr12:57675000-57701000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:57675400-57707000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:57676200-57700000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:57676200-57700000	Strong transcription	Fetal Intestine Large	intestine
23	chr12:57677600-57713000	Weak transcription	Stomach Mucosa	stomach
24	chr12:57678000-57699400	Weak transcription	A549	lung
25	chr12:57678000-57713000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:57679200-57699800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:57680000-57698800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:57682400-57700200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:57682800-57698600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:57682800-57700200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:57684000-57699800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:57684200-57699000	Weak transcription	Fetal Brain Male	brain
33	chr12:57684600-57700200	Strong transcription	Primary B cells from cord blood	blood
34	chr12:57684800-57700000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:57685400-57700000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:57685400-57700400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:57689200-57701800	Weak transcription	Brain Substantia Nigra	brain
38	chr12:57689200-57703200	Weak transcription	Hela-S3	cervix
39	chr12:57689600-57703000	Weak transcription	HMEC	breast
40	chr12:57690200-57699400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:57690400-57703200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:57690800-57698000	Weak transcription	Esophagus	oesophagus
43	chr12:57690800-57702600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:57690800-57705400	Weak transcription	Spleen	Spleen
45	chr12:57691000-57736200	Weak transcription	Right Atrium	heart
46	chr12:57692000-57703000	Weak transcription	NH-A	brain
47	chr12:57692200-57699200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:57692600-57697600	Strong transcription	Thymus	Thymus
49	chr12:57692800-57697600	Strong transcription	Fetal Stomach	stomach
50	chr12:57692800-57698400	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links