Variant report

Variant	rs12587583
Chromosome Location	chr14:69510441-69510442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69504422..69507358-chr14:69508879..69511159,3	K562	blood:
2	chr14:69443082..69446531-chr14:69508749..69512052,3	MCF-7	breast:
3	chr14:69504745..69507053-chr14:69509221..69511186,2	K562	blood:
4	chr14:69509516..69511867-chr14:69516785..69518718,2	K562	blood:
5	chr14:69509691..69512207-chr14:69526446..69528305,2	MCF-7	breast:
6	chr14:69504480..69506632-chr14:69509556..69511632,2	MCF-7	breast:
7	chr14:69510349..69511857-chr14:69516882..69518965,2	K562	blood:

Variant related genes	Relation type
ENSG00000072110	Chromatin interaction
ENSG00000259062	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10083451	0.83[GIH][hapmap]
rs10130013	0.83[GIH][hapmap]
rs10139873	0.83[GIH][hapmap]
rs10143302	0.83[GIH][hapmap]
rs10147369	0.83[GIH][hapmap]
rs10148614	0.89[CHB][hapmap]
rs11158782	0.83[GIH][hapmap]
rs11158787	0.83[GIH][hapmap]
rs11158790	0.83[GIH][hapmap]
rs11158795	0.80[GIH][hapmap]
rs11622889	0.81[GIH][hapmap]
rs11628353	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12431846	0.85[GIH][hapmap]
rs12432046	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12432645	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[AFR][1000 genomes]
rs12434775	0.85[GIH][hapmap]
rs12435594	0.83[GIH][hapmap]
rs12586650	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12589028	0.83[GIH][hapmap]
rs12884238	1.00[ASW][hapmap]
rs12889047	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894822	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17758220	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2001998	0.83[GIH][hapmap]
rs2056153	0.83[GIH][hapmap]
rs28613298	0.83[GIH][hapmap]
rs34075727	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34227963	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34471700	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35286356	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35700516	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36114431	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7150412	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7151437	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7157918	0.91[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs8008184	0.83[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12587583	WDR22	Cis_1M	lymphoblastoid	RTeQTL
rs12587583	SPTB	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69505800-69510600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:69505800-69510800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:69506000-69511200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:69506600-69511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:69507200-69510800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:69508400-69511200	Enhancers	Duodenum Mucosa	Duodenum
7	chr14:69508600-69510800	Enhancers	Brain Angular Gyrus	brain
8	chr14:69508600-69511600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr14:69508600-69512200	Enhancers	HSMMtube	muscle
10	chr14:69508600-69513200	Enhancers	Fetal Intestine Small	intestine
11	chr14:69508600-69513400	Enhancers	Fetal Intestine Large	intestine
12	chr14:69508800-69513000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr14:69508800-69513800	Enhancers	Brain Hippocampus Middle	brain
14	chr14:69508800-69513800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:69508800-69513800	Enhancers	NHDF-Ad	bronchial
16	chr14:69508800-69514600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr14:69508800-69516600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:69508800-69518000	Enhancers	Fetal Muscle Leg	muscle
19	chr14:69509000-69510800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr14:69509000-69510800	Enhancers	Stomach Mucosa	stomach
21	chr14:69509000-69511800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr14:69509000-69513800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr14:69509200-69510600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr14:69509200-69510800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr14:69509200-69512800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr14:69509400-69510600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr14:69509400-69512400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:69509400-69513800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr14:69509400-69513800	Enhancers	Ovary	ovary
30	chr14:69509400-69514000	Enhancers	NH-A	brain
31	chr14:69509600-69510600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr14:69509600-69511000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr14:69509600-69511400	Enhancers	HSMM	muscle
34	chr14:69509600-69512000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:69509600-69512200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr14:69509600-69512400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr14:69509600-69513000	Enhancers	Pancreas	Pancrea
38	chr14:69509600-69513400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr14:69509600-69513800	Enhancers	Colonic Mucosa	Colon
40	chr14:69509600-69513800	Enhancers	Esophagus	oesophagus
41	chr14:69509600-69513800	Enhancers	Fetal Muscle Trunk	muscle
42	chr14:69509600-69513800	Enhancers	Psoas Muscle	Psoas
43	chr14:69509600-69513800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr14:69509600-69513800	Enhancers	Rectal Smooth Muscle	rectum
45	chr14:69509600-69514400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr14:69509600-69515600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr14:69509600-69516400	Enhancers	HUVEC	blood vessel
48	chr14:69509800-69510600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:69509800-69510600	Bivalent Enhancer	HepG2	liver
50	chr14:69509800-69510800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links