Variant report

Variant	rs12316287
Chromosome Location	chr12:64377169-64377170
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64373746..64376340-chr12:64376425..64378945,3	MCF-7	breast:
2	chr12:64376417..64378425-chr12:64384160..64386437,2	K562	blood:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11175222	1.00[AMR][1000 genomes]
rs11175223	1.00[AMR][1000 genomes]
rs11175224	1.00[AMR][1000 genomes]
rs12296441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12297450	1.00[AMR][1000 genomes]
rs12302441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12305930	1.00[AMR][1000 genomes]
rs12307017	1.00[EUR][1000 genomes]
rs12312286	1.00[AMR][1000 genomes]
rs12313251	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12315032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318085	0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320688	1.00[EUR][1000 genomes]
rs17099997	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17100007	1.00[EUR][1000 genomes]
rs17100009	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17100013	1.00[EUR][1000 genomes]
rs2135946	1.00[MEX][hapmap]
rs55801058	1.00[EUR][1000 genomes]
rs57074356	1.00[EUR][1000 genomes]
rs57138272	1.00[EUR][1000 genomes]
rs57140731	1.00[EUR][1000 genomes]
rs57540857	1.00[EUR][1000 genomes]
rs57937852	1.00[EUR][1000 genomes]
rs58129443	1.00[EUR][1000 genomes]
rs59161915	1.00[EUR][1000 genomes]
rs60392489	1.00[EUR][1000 genomes]
rs74097504	1.00[EUR][1000 genomes]
rs74097515	1.00[EUR][1000 genomes]
rs74097516	1.00[EUR][1000 genomes]
rs74097517	1.00[EUR][1000 genomes]
rs74097545	1.00[EUR][1000 genomes]
rs74097547	1.00[EUR][1000 genomes]
rs74099369	1.00[EUR][1000 genomes]
rs74099375	1.00[EUR][1000 genomes]
rs74099376	1.00[EUR][1000 genomes]
rs74099377	1.00[EUR][1000 genomes]
rs74099378	1.00[EUR][1000 genomes]
rs74099379	1.00[EUR][1000 genomes]
rs74099380	1.00[EUR][1000 genomes]
rs74099381	1.00[EUR][1000 genomes]
rs74099382	1.00[EUR][1000 genomes]
rs74099383	1.00[EUR][1000 genomes]
rs74099384	1.00[EUR][1000 genomes]
rs74099385	1.00[EUR][1000 genomes]
rs74099392	1.00[EUR][1000 genomes]
rs74099393	1.00[EUR][1000 genomes]
rs74099395	1.00[EUR][1000 genomes]
rs74099398	1.00[EUR][1000 genomes]
rs74099400	1.00[EUR][1000 genomes]
rs7961633	1.00[EUR][1000 genomes]
rs7961964	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7976142	1.00[EUR][1000 genomes]
rs7976369	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7977480	1.00[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	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	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2577852	chr12:64376290-64377762	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12316287	CLIC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64362600-64385600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:64362800-64377600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:64362800-64378800	Weak transcription	Pancreas	Pancrea
5	chr12:64362800-64396000	Weak transcription	Psoas Muscle	Psoas
6	chr12:64364200-64385800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:64365000-64383000	Weak transcription	Stomach Mucosa	stomach
8	chr12:64365800-64378600	Weak transcription	Fetal Intestine Small	intestine
9	chr12:64365800-64379400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:64366400-64383600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:64370800-64384400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:64371800-64385800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:64372000-64383200	Weak transcription	Fetal Kidney	kidney
14	chr12:64372400-64382000	Weak transcription	HSMM	muscle
15	chr12:64372800-64380600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:64373800-64383000	Weak transcription	HMEC	breast
17	chr12:64374000-64377200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:64374400-64377600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:64374400-64377800	Weak transcription	NHEK	skin
20	chr12:64374400-64379000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:64374600-64378600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:64375000-64377200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:64375200-64377200	Enhancers	NHLF	lung
24	chr12:64375400-64377200	Enhancers	Colon Smooth Muscle	Colon
25	chr12:64375400-64377200	Enhancers	Fetal Brain Female	brain
26	chr12:64375400-64383200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:64375600-64378800	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:64375600-64383200	Weak transcription	Fetal Lung	lung
29	chr12:64375600-64384600	Weak transcription	Hela-S3	cervix
30	chr12:64375800-64377200	Enhancers	NHDF-Ad	bronchial
31	chr12:64375800-64385600	Weak transcription	Adipose Nuclei	Adipose
32	chr12:64376000-64377200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:64376000-64377200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:64376200-64377200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:64376200-64377200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:64376200-64377200	Enhancers	Brain Hippocampus Middle	brain
37	chr12:64376200-64377200	Enhancers	Brain Substantia Nigra	brain
38	chr12:64376200-64385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:64376400-64377200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:64376400-64377200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:64376400-64377200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:64376400-64377200	Enhancers	Brain Cingulate Gyrus	brain
43	chr12:64376400-64377200	Enhancers	Brain Germinal Matrix	brain
44	chr12:64376400-64377200	Genic enhancers	A549	lung
45	chr12:64376400-64377600	Enhancers	Ovary	ovary
46	chr12:64376600-64377200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:64376600-64377200	Enhancers	Rectal Smooth Muscle	rectum
48	chr12:64376800-64377200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr12:64376800-64377200	Enhancers	HSMMtube	muscle
50	chr12:64376800-64377200	Enhancers	NH-A	brain

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