Variant report

Variant	rs888152
Chromosome Location	chr12:12240665-12240666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1641726	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741793	0.93[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4254157	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488501	0.91[EUR][1000 genomes]
rs7959374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7972613	0.94[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv975623	chr12:12238184-12243964	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv557583	chr12:12238317-12253591	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs888152	WBP11	cis	parietal	SCAN
rs888152	GPRC5D	cis	cerebellum	SCAN
rs888152	MGP	cis	parietal	SCAN
rs888152	LOH12CR1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12225000-12255000	Weak transcription	Small Intestine	intestine
2	chr12:12226600-12245000	Weak transcription	Fetal Brain Male	brain
3	chr12:12232800-12257000	Weak transcription	HSMMtube	muscle
4	chr12:12234800-12259600	Weak transcription	Aorta	Aorta
5	chr12:12235200-12242000	Weak transcription	NHLF	lung
6	chr12:12235400-12243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:12235400-12244600	Weak transcription	Colonic Mucosa	Colon
8	chr12:12235400-12245000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:12235400-12245200	Weak transcription	Pancreas	Pancrea
10	chr12:12235400-12260200	Weak transcription	Gastric	stomach
11	chr12:12235400-12260800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:12235600-12240800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:12237400-12259800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:12238000-12245000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:12238400-12241000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:12238400-12241000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:12238600-12241200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:12238600-12241800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:12238600-12242000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:12239000-12241200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:12239200-12241000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:12239200-12241000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr12:12239200-12241200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:12239200-12241200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr12:12239200-12241800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:12239400-12241000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:12239400-12241200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:12239400-12241800	Enhancers	HepG2	liver
30	chr12:12239600-12240800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:12239600-12240800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:12239600-12240800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:12239600-12241000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:12239600-12241400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:12239600-12249200	Strong transcription	Fetal Intestine Small	intestine
36	chr12:12239800-12240800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:12239800-12241000	Enhancers	Brain Anterior Caudate	brain
38	chr12:12240000-12241000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:12240000-12242000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:12240200-12241800	Strong transcription	Fetal Stomach	stomach
41	chr12:12240200-12241800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:12240200-12242200	Strong transcription	Fetal Intestine Large	intestine
43	chr12:12240400-12244200	Weak transcription	Fetal Lung	lung
44	chr12:12240400-12254200	Weak transcription	Stomach Mucosa	stomach
45	chr12:12240600-12240800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr12:12240600-12241600	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:12240600-12245400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:12240600-12245400	Weak transcription	Brain Germinal Matrix	brain
49	chr12:12240600-12256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links