Variant report

Variant	rs7972986
Chromosome Location	chr12:42481732-42481733
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	chr12:42480575..42482841-chr12:42486145..42488403,3	K562	blood:
2	chr12:42480575..42482340-chr12:42486145..42488403,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10492386	0.93[JPT][hapmap]
rs10492387	0.85[JPT][hapmap]
rs10785332	0.96[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs10880222	0.82[AMR][1000 genomes]
rs10880252	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10880263	0.93[JPT][hapmap];0.84[YRI][hapmap]
rs10880274	0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap]
rs10880276	0.91[YRI][hapmap]
rs11181283	0.81[AMR][1000 genomes]
rs11181317	0.89[AMR][1000 genomes]
rs11181322	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181325	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181332	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181344	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11181347	1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs11181356	0.96[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap]
rs11181359	0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs11181384	0.93[JPT][hapmap]
rs11181388	0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs12231330	0.82[AMR][1000 genomes]
rs12579560	0.97[GIH][hapmap];0.86[JPT][hapmap]
rs1532220	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17090898	0.85[AMR][1000 genomes]
rs17091018	0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs17494245	0.85[AMR][1000 genomes]
rs1988893	0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs3852593	0.82[JPT][hapmap];0.90[MEX][hapmap]
rs3852594	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56085053	0.82[AMR][1000 genomes]
rs60631072	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61942482	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61942484	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7296847	0.93[GIH][hapmap];0.86[JPT][hapmap]
rs7965273	1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]

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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1047830	chr12:42466192-42497603	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2025559	chr12:42481619-42491335	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7972986	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs7972986	ZCRB1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42464600-42484000	Weak transcription	HSMM	muscle
2	chr12:42468400-42490200	Weak transcription	Spleen	Spleen
3	chr12:42469400-42491800	Weak transcription	Ovary	ovary
4	chr12:42470400-42484000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:42470600-42484000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:42470600-42491400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:42470800-42485600	Weak transcription	Aorta	Aorta
8	chr12:42471000-42504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:42471200-42483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:42471400-42485600	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:42471800-42483400	Weak transcription	Fetal Stomach	stomach
12	chr12:42471800-42486600	Weak transcription	Fetal Intestine Small	intestine
13	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
14	chr12:42472200-42487800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:42472800-42489000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:42473600-42483600	Weak transcription	Adipose Nuclei	Adipose
17	chr12:42473600-42484000	Weak transcription	HUVEC	blood vessel
18	chr12:42473600-42484200	Weak transcription	Primary T cells from cord blood	blood
19	chr12:42473800-42484000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:42474000-42484000	Weak transcription	NH-A	brain
21	chr12:42474000-42484200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:42474000-42496000	Weak transcription	Fetal Intestine Large	intestine
23	chr12:42474200-42484000	Weak transcription	Osteobl	bone
24	chr12:42474200-42486000	Weak transcription	GM12878-XiMat	blood
25	chr12:42474200-42487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:42474200-42490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:42474600-42482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
30	chr12:42474800-42487600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:42474800-42487600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:42474800-42491800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:42475000-42484200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:42475000-42491800	Weak transcription	Brain Substantia Nigra	brain
35	chr12:42475400-42485600	Weak transcription	Left Ventricle	heart
36	chr12:42476000-42485600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:42476000-42524400	Weak transcription	Gastric	stomach
38	chr12:42476200-42487000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
40	chr12:42476400-42482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:42476400-42487400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:42476400-42487600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:42476400-42489800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:42476600-42523800	Weak transcription	Hela-S3	cervix
45	chr12:42476800-42483400	Weak transcription	Fetal Kidney	kidney
46	chr12:42476800-42484200	Weak transcription	NHEK	skin
47	chr12:42477000-42484000	Weak transcription	NHDF-Ad	bronchial
48	chr12:42477400-42482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:42477600-42482400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:42477600-42490400	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links