Variant report

Variant	rs12532878
Chromosome Location	chr7:100212254-100212255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100210802..100213232-chr7:100246943..100248690,2	K562	blood:
2	chr7:100207856..100214217-chr7:100235772..100240956,9	K562	blood:
3	chr7:100025028..100029218-chr7:100206824..100213289,7	K562	blood:
4	chr7:100206101..100213131-chr7:100214394..100226559,23	K562	blood:
5	chr7:100207807..100212872-chr7:100269575..100273736,11	MCF-7	breast:
6	chr7:100210571..100212483-chr7:100283405..100286234,2	K562	blood:
7	chr7:100207856..100215304-chr7:100235701..100242038,10	K562	blood:
8	chr7:100208328..100213557-chr7:100269728..100273649,8	MCF-7	breast:
9	chr7:100181910..100186072-chr7:100207984..100213440,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000146834	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000146830	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000172354	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10487157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953298	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10953301	0.81[CHB][hapmap]
rs11520986	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs11764045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766643	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11767547	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11770389	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11974395	0.81[CHB][hapmap];0.84[MEX][hapmap]
rs11979818	0.85[MEX][hapmap]
rs11983334	0.84[MEX][hapmap]
rs11983745	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13227444	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2075671	0.89[MEX][hapmap]
rs2075672	0.86[JPT][hapmap]
rs2075674	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2231170	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2231172	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs2272572	0.81[CHB][hapmap]
rs28584500	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41303510	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4727459	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs4729597	0.86[JPT][hapmap]
rs4729601	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4729602	0.81[CHB][hapmap];0.89[MEX][hapmap]
rs4729606	0.80[MEX][hapmap]
rs62482237	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62482238	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62482239	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62482242	0.84[AMR][1000 genomes]
rs6958696	0.83[AMR][1000 genomes]
rs6969584	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6969697	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73156234	0.83[AMR][1000 genomes]
rs73407376	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7385804	0.86[JPT][hapmap]
rs7457024	0.98[ASN][1000 genomes]
rs7786877	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs7812123	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7812235	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
3	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
4	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
5	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv5868	chr7:100169998-100214646	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases
10	nsv888790	chr7:100200674-100232387	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12532878	POLR2J	cis	parietal	SCAN
rs12532878	FAM185A	cis	cerebellum	SCAN
rs12532878	LHFPL3	cis	cerebellum	SCAN
rs12532878	SERPINE1	cis	cerebellum	SCAN
rs12532878	MOSPD3	cis	Whole Blood	GTEx
rs12532878	DLX5	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100210600-100224400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:100211000-100214400	Weak transcription	Gastric	stomach
3	chr7:100211000-100217400	Weak transcription	Aorta	Aorta
4	chr7:100211000-100217400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:100211000-100223800	Weak transcription	Fetal Kidney	kidney
6	chr7:100211000-100224600	Weak transcription	Small Intestine	intestine
7	chr7:100211200-100213000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:100211200-100214000	Weak transcription	Brain Anterior Caudate	brain
9	chr7:100211200-100214000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:100211200-100214600	Weak transcription	Right Atrium	heart
11	chr7:100211200-100215400	Weak transcription	Fetal Intestine Large	intestine
12	chr7:100211200-100215400	Weak transcription	Hela-S3	cervix
13	chr7:100211200-100218600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:100211200-100221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:100211200-100221800	Weak transcription	HSMMtube	muscle
16	chr7:100211200-100223800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:100211200-100224000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:100211200-100224000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:100211200-100224000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:100211200-100224000	Weak transcription	Brain Angular Gyrus	brain
21	chr7:100211200-100224000	Weak transcription	Lung	lung
22	chr7:100211200-100224000	Weak transcription	Psoas Muscle	Psoas
23	chr7:100211200-100224000	Weak transcription	Right Ventricle	heart
24	chr7:100211200-100224400	Weak transcription	Left Ventricle	heart
25	chr7:100211400-100212400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr7:100211400-100215400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:100211400-100218000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:100211400-100218000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr7:100211400-100218000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:100211400-100218200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr7:100211400-100220800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:100211400-100221800	Weak transcription	Esophagus	oesophagus
33	chr7:100211400-100223400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:100211400-100223800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:100211400-100224000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:100211400-100224000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr7:100211400-100224000	Weak transcription	Brain Substantia Nigra	brain
38	chr7:100211400-100224000	Weak transcription	Colonic Mucosa	Colon
39	chr7:100211400-100224000	Weak transcription	HSMM	muscle
40	chr7:100211400-100224000	Weak transcription	HUVEC	blood vessel
41	chr7:100211400-100224600	Weak transcription	Spleen	Spleen
42	chr7:100211400-100230400	Weak transcription	Pancreas	Pancrea
43	chr7:100211600-100212400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:100211600-100212600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:100211600-100212800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr7:100211600-100213600	Strong transcription	Fetal Lung	lung
47	chr7:100211600-100214600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:100211600-100216000	Strong transcription	Fetal Stomach	stomach
49	chr7:100211600-100219200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr7:100211600-100220200	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links