Variant report

Variant	rs12613853
Chromosome Location	chr2:178997647-178997648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178996756..178997699-chr2:179073384..179074155,3	MCF-7	breast:
2	chr2:178991568..178995332-chr2:178996165..178998325,3	MCF-7	breast:
3	chr2:178997047..178997691-chr2:179278995..179280004,3	K562	blood:
4	chr2:178977795..178981676-chr2:178993113..178997821,5	K562	blood:
5	chr2:178996751..178997649-chr2:179144316..179145071,2	MCF-7	breast:
6	chr2:178996470..178998861-chr2:179058707..179060776,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1025446	0.90[JPT][hapmap]
rs10930827	0.91[MEX][hapmap]
rs12617847	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12619532	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13005772	0.92[ASN][1000 genomes]
rs13006877	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs1435572	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs16866111	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16866116	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16866118	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2276622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2366366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334062	0.95[JPT][hapmap];0.80[MEX][hapmap]
rs334068	0.95[JPT][hapmap]
rs62176035	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6705312	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6753254	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7564892	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv518790	chr2:178963445-179000291	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12613853	FKBP7	cis	parietal	SCAN
rs12613853	HOXD12	cis	parietal	SCAN
rs12613853	GPR155	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178978000-179001000	Weak transcription	Lung	lung
2	chr2:178978000-179002200	Weak transcription	Esophagus	oesophagus
3	chr2:178978000-179003200	Weak transcription	Spleen	Spleen
4	chr2:178978000-179003800	Weak transcription	Aorta	Aorta
5	chr2:178978000-179016400	Weak transcription	Gastric	stomach
6	chr2:178978200-179002800	Weak transcription	Fetal Stomach	stomach
7	chr2:178978400-179001200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:178978400-179001400	Weak transcription	Brain Substantia Nigra	brain
9	chr2:178978400-179001600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:178978400-179001800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:178978600-178998400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:178978600-179001800	Weak transcription	Hela-S3	cervix
13	chr2:178978600-179003000	Weak transcription	Right Ventricle	heart
14	chr2:178978600-179003600	Weak transcription	Fetal Heart	heart
15	chr2:178978800-179001000	Weak transcription	Pancreas	Pancrea
16	chr2:178978800-179004000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:178979000-179005400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:178979600-178998800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:178987200-179005800	Weak transcription	Psoas Muscle	Psoas
20	chr2:178987400-179002800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:178987800-179017000	Weak transcription	Fetal Lung	lung
22	chr2:178988400-179001800	Weak transcription	NHDF-Ad	bronchial
23	chr2:178988400-179002000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:178988600-179002800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:178989000-178999200	Weak transcription	NHLF	lung
26	chr2:178989400-179000400	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:178989600-178997800	Weak transcription	Small Intestine	intestine
28	chr2:178989600-179000200	Weak transcription	Thymus	Thymus
29	chr2:178989600-179000400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:178989600-179001400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:178989600-179001600	Weak transcription	Ovary	ovary
32	chr2:178990200-178998000	Weak transcription	HSMM	muscle
33	chr2:178990200-179007000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:178990400-179003000	Weak transcription	HMEC	breast
35	chr2:178990600-178998400	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:178990600-178999800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:178990600-179001800	Weak transcription	HepG2	liver
38	chr2:178990800-178998600	Weak transcription	A549	lung
39	chr2:178990800-178998800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:178990800-178999400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:178990800-179001400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:178990800-179001800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:178990800-179002000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:178990800-179003800	Weak transcription	GM12878-XiMat	blood
45	chr2:178991000-179000000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:178991000-179001400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:178991000-179009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:178991200-179007400	Weak transcription	Osteobl	bone
49	chr2:178991800-179003600	Weak transcription	Left Ventricle	heart
50	chr2:178992000-178999400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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