Variant report

Variant	rs7793919
Chromosome Location	chr7:4769030-4769031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4768370..4770170-chr7:4773458..4776418,2	K562	blood:
2	chr7:4752699..4756529-chr7:4767916..4770424,4	K562	blood:
3	chr7:4680348..4683879-chr7:4764377..4769101,7	MCF-7	breast:
4	chr7:4760865..4762591-chr7:4767283..4769711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164916	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10228886	1.00[CHB][hapmap]
rs10257680	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10261971	0.88[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10262715	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10277273	0.82[EUR][1000 genomes]
rs13232425	0.90[ASN][1000 genomes]
rs3087749	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs35735269	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4724033	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6463014	0.85[ASN][1000 genomes]
rs6944865	0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs6973046	0.86[JPT][hapmap]
rs6975499	0.85[ASN][1000 genomes]
rs7781115	0.81[EUR][1000 genomes]
rs7781456	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7784748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.84[EUR][1000 genomes]
rs7786525	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv508442	chr7:4623264-4769628	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv887381	chr7:4769030-4880954	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7793919	ZNF12	cis	parietal	SCAN
rs7793919	PMS2CL	cis	cerebellum	SCAN
rs7793919	RAC1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4753400-4774800	Weak transcription	K562	blood
2	chr7:4756400-4776800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:4757200-4778800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:4765200-4769800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:4765400-4778200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:4765600-4769800	Weak transcription	Gastric	stomach
7	chr7:4765600-4769800	Weak transcription	Thymus	Thymus
8	chr7:4765600-4770000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr7:4765600-4770000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:4765600-4771600	Weak transcription	NHEK	skin
11	chr7:4765600-4773200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:4765600-4777600	Strong transcription	Fetal Intestine Small	intestine
13	chr7:4765600-4778200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:4765600-4778200	Weak transcription	Aorta	Aorta
15	chr7:4765600-4778200	Weak transcription	Ovary	ovary
16	chr7:4765600-4778400	Weak transcription	Brain Germinal Matrix	brain
17	chr7:4765600-4783200	Weak transcription	Fetal Brain Male	brain
18	chr7:4765600-4784000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:4765800-4773400	Weak transcription	Psoas Muscle	Psoas
20	chr7:4765800-4778200	Weak transcription	Osteobl	bone
21	chr7:4765800-4778400	Weak transcription	Fetal Kidney	kidney
22	chr7:4765800-4782400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:4766000-4769800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:4766000-4769800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:4766000-4770000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:4766000-4770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:4766000-4771800	Weak transcription	Primary B cells from cord blood	blood
28	chr7:4766000-4771800	Weak transcription	GM12878-XiMat	blood
29	chr7:4766000-4772000	Weak transcription	A549	lung
30	chr7:4766000-4773000	Weak transcription	NH-A	brain
31	chr7:4766000-4773400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:4766000-4773400	Weak transcription	HSMMtube	muscle
33	chr7:4766000-4778000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:4766000-4778000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:4766000-4778000	Weak transcription	NHDF-Ad	bronchial
36	chr7:4766000-4778200	Weak transcription	Fetal Brain Female	brain
37	chr7:4766000-4778200	Weak transcription	HSMM	muscle
38	chr7:4766000-4778800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:4766000-4783600	Weak transcription	HMEC	breast
40	chr7:4766200-4769800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:4766200-4770200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:4766200-4778200	Weak transcription	Stomach Mucosa	stomach
43	chr7:4766400-4769800	Weak transcription	Left Ventricle	heart
44	chr7:4766400-4770000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:4766400-4770000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:4766400-4770000	Weak transcription	Adipose Nuclei	Adipose
47	chr7:4766400-4775000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:4766400-4778000	Weak transcription	HUVEC	blood vessel
49	chr7:4766600-4769600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:4766600-4769600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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