Variant report

Variant	rs12668144
Chromosome Location	chr7:39682385-39682386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39678677..39680860-chr7:39681239..39684252,3	K562	blood:
2	chr7:39672032..39673667-chr7:39681503..39683307,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10253933	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10267545	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10486803	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10486805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11765970	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11773499	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs11773617	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12669963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12701754	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12701755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12701756	0.83[ASN][1000 genomes]
rs12701757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs12701759	0.82[EUR][1000 genomes]
rs13244194	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13247563	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17417049	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17417084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34063025	1.00[ASN][1000 genomes]
rs34910913	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35314132	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35774126	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779200	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62453003	0.82[EUR][1000 genomes]
rs6462940	1.00[ASN][1000 genomes]
rs6968684	1.00[ASN][1000 genomes]
rs6976944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6977082	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778955	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7779169	0.83[ASN][1000 genomes]
rs7782931	0.82[EUR][1000 genomes]
rs7792940	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7797693	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9648483	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12668144	C7orf11	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39666200-39694400	Weak transcription	Fetal Brain Female	brain
2	chr7:39667200-39698800	Weak transcription	Fetal Kidney	kidney
3	chr7:39671800-39693800	Weak transcription	A549	lung
4	chr7:39672200-39684000	Weak transcription	NHLF	lung
5	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
6	chr7:39672400-39683200	Weak transcription	Pancreas	Pancrea
7	chr7:39674000-39690200	Weak transcription	NH-A	brain
8	chr7:39674000-39690800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:39674200-39683200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:39674200-39683800	Weak transcription	Spleen	Spleen
11	chr7:39674200-39690000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:39674200-39691400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:39674200-39696000	Weak transcription	Thymus	Thymus
14	chr7:39674400-39683800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:39674400-39685400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:39674800-39682400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr7:39675200-39682800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:39675200-39683800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:39675200-39708800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:39675600-39688200	Weak transcription	Fetal Stomach	stomach
21	chr7:39675600-39701400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:39675800-39691600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:39676000-39682600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:39676600-39683400	Weak transcription	Osteobl	bone
25	chr7:39676600-39683600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:39676600-39690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:39676600-39694400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:39676600-39694400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:39676600-39694400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:39676800-39685200	Weak transcription	HepG2	liver
31	chr7:39677400-39694200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:39677600-39683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:39678000-39687800	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:39678800-39694400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:39679600-39682400	Weak transcription	HMEC	breast
36	chr7:39679600-39695800	Weak transcription	Primary B cells from cord blood	blood
37	chr7:39679800-39683600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:39680000-39683000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:39680000-39683000	Weak transcription	Left Ventricle	heart
40	chr7:39680000-39683200	Weak transcription	NHEK	skin
41	chr7:39680000-39700800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:39680000-39701000	Weak transcription	Esophagus	oesophagus
43	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr7:39680200-39682600	Enhancers	Small Intestine	intestine
45	chr7:39680400-39682600	Enhancers	K562	blood
46	chr7:39680400-39682800	Enhancers	Stomach Mucosa	stomach
47	chr7:39680400-39687400	Weak transcription	Primary T cells from cord blood	blood
48	chr7:39680600-39682600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr7:39680600-39683400	Weak transcription	GM12878-XiMat	blood
50	chr7:39680600-39683800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links