Variant report

Variant	rs11168857
Chromosome Location	chr12:49490309-49490310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49490293-49490838	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49490226..49493443-chr12:49495153..49498719,5	MCF-7	breast:
2	chr12:49453076..49457977-chr12:49485062..49491403,12	K562	blood:
3	chr12:49490023..49493728-chr12:49522829..49525742,6	MCF-7	breast:
4	chr12:49478072..49490419-chr12:49518907..49527034,52	K562	blood:
5	chr12:49477289..49493962-chr12:49512467..49528127,64	K562	blood:
6	chr12:49482462..49486545-chr12:49487319..49491529,4	MCF-7	breast:
7	chr12:49450480..49457103-chr12:49487982..49492074,8	K562	blood:
8	chr12:49452588..49458658-chr12:49486666..49491439,6	MCF-7	breast:
9	chr12:49489085..49493906-chr12:49497574..49505715,14	K562	blood:

No data

Variant related genes	Relation type
DHH	TF binding region
ENSG00000257346	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1039225	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap]
rs10747561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10747562	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10747563	0.94[CHB][hapmap]
rs10783302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs10783304	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10783307	0.83[CEU][hapmap]
rs10783308	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs10875924	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10875928	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs10875931	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs10875934	0.94[CHB][hapmap]
rs11168862	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168884	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs11168893	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs11168910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap]
rs12229524	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1476137	0.88[CEU][hapmap]
rs1874908	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs1991427	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2047101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2162644	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2279596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2334930	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs2753	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs3741621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7306084	0.94[CHB][hapmap]
rs731350	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7954521	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7954530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs7957983	0.81[EUR][1000 genomes]
rs7957998	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7958241	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7958572	0.92[CEU][hapmap]
rs7959497	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs7969967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7978448	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7978659	0.86[EUR][1000 genomes]
rs9325145	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11168857	TFCP2	cis	parietal	SCAN
rs11168857	C19orf55	trans	cerebellum	SCAN
rs11168857	CCDC65	cis	Artery Aorta	GTEx
rs11168857	RHEBL1	cis	parietal	SCAN
rs11168857	POU6F1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49482800-49499200	Weak transcription	Hela-S3	cervix
2	chr12:49485800-49490800	Weak transcription	Aorta	Aorta
3	chr12:49486400-49490600	Weak transcription	HSMM	muscle
4	chr12:49487600-49490600	Weak transcription	Dnd41	blood
5	chr12:49488600-49490400	Weak transcription	Primary B cells from cord blood	blood
6	chr12:49488600-49490400	Weak transcription	Brain Angular Gyrus	brain
7	chr12:49488600-49490400	Weak transcription	Colonic Mucosa	Colon
8	chr12:49488600-49490400	Weak transcription	Ovary	ovary
9	chr12:49488600-49490600	Weak transcription	Pancreas	Pancrea
10	chr12:49488600-49490800	Weak transcription	Gastric	stomach
11	chr12:49488600-49491200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:49488600-49491200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:49488600-49493800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:49488600-49494000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:49488800-49490400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:49488800-49490400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:49488800-49491000	Weak transcription	A549	lung
18	chr12:49489000-49490400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:49489000-49490400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:49489000-49490400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:49489000-49490400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:49489000-49490400	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:49489000-49490400	Weak transcription	Placenta	Placenta
24	chr12:49489000-49490400	Weak transcription	HSMMtube	muscle
25	chr12:49489000-49490600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:49489000-49490600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:49489000-49490600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:49489000-49490600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:49489000-49490600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:49489000-49490600	Weak transcription	Esophagus	oesophagus
31	chr12:49489000-49490600	Weak transcription	Lung	lung
32	chr12:49489000-49490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:49489000-49490600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:49489000-49491000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:49489000-49491000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:49489000-49491400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:49489000-49491400	Weak transcription	HepG2	liver
38	chr12:49489000-49491800	Weak transcription	Psoas Muscle	Psoas
39	chr12:49489000-49493200	Weak transcription	Small Intestine	intestine
40	chr12:49489000-49493800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:49489000-49493800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:49489000-49494000	Weak transcription	GM12878-XiMat	blood
43	chr12:49489000-49494800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:49489200-49490400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:49489200-49490400	Weak transcription	Brain Anterior Caudate	brain
46	chr12:49489200-49490400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:49489200-49490600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:49489200-49490600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:49489200-49490600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:49489200-49490600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links