Variant report

Variant	rs6973046
Chromosome Location	chr7:4765018-4765019
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:4750973..4755247-chr7:4763506..4767347,8	MCF-7	breast:
2	chr7:4721561..4725553-chr7:4763080..4767294,4	MCF-7	breast:
3	chr7:4720287..4723602-chr7:4763123..4767792,8	MCF-7	breast:
4	chr7:4762980..4766999-chr7:4782747..4785912,5	MCF-7	breast:
5	chr7:4728262..4730574-chr7:4763731..4766001,2	MCF-7	breast:
6	chr7:4756833..4759526-chr7:4763472..4765275,2	MCF-7	breast:
7	chr7:4762748..4765277-chr7:4778868..4780947,2	MCF-7	breast:
8	chr7:4763844..4765734-chr7:4769796..4771945,2	K562	blood:
9	chr7:4759871..4762762-chr7:4764322..4767254,4	MCF-7	breast:
10	chr7:4680335..4683615-chr7:4763536..4766738,3	MCF-7	breast:
11	chr7:4723706..4725532-chr7:4763308..4765301,2	MCF-7	breast:
12	chr7:4680348..4683879-chr7:4764377..4769101,7	MCF-7	breast:
13	chr7:4763802..4765803-chr7:4775724..4778098,2	MCF-7	breast:
14	chr7:4762343..4766286-chr7:4781806..4786084,5	MCF-7	breast:
15	chr7:4760150..4762017-chr7:4764864..4767459,2	K562	blood:
16	chr7:4747915..4749445-chr7:4764034..4766234,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164916	Chromatin interaction
ENSG00000238781	Chromatin interaction

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

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

rs_ID	r²[population]
rs10228886	0.93[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10261971	0.89[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs11765781	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs13228233	0.86[JPT][hapmap]
rs13232425	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3087749	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4077986	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4492258	0.98[ASN][1000 genomes]
rs4523152	0.86[JPT][hapmap]
rs4540325	0.86[JPT][hapmap]
rs4720401	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs4720402	0.88[CEU][hapmap]
rs4724033	1.00[JPT][hapmap]
rs6944865	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6946034	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6950090	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7781456	1.00[JPT][hapmap]
rs7793919	0.86[JPT][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6973046	PAPOLB	cis	cerebellum	SCAN
rs6973046	RAC1	cis	parietal	SCAN
rs6973046	ZNF12	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr7:4761800-4768000	Enhancers	Fetal Heart	heart
5	chr7:4764000-4765800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr7:4764000-4765800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:4764000-4766000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:4764000-4766200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr7:4764000-4766400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:4764200-4765400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:4764200-4765400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:4764200-4765400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr7:4764200-4765400	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr7:4764200-4765400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr7:4764200-4765400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:4764200-4765600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:4764200-4765600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:4764200-4765600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr7:4764200-4765600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr7:4764200-4765600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:4764200-4765600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:4764200-4765600	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr7:4764200-4765600	Flanking Active TSS	Fetal Lung	lung
24	chr7:4764200-4765600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr7:4764200-4765600	Active TSS	Hela-S3	cervix
26	chr7:4764200-4765600	Flanking Active TSS	NH-A	brain
27	chr7:4764200-4765800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:4764200-4765800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr7:4764200-4765800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr7:4764200-4765800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:4764200-4765800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:4764200-4765800	Flanking Active TSS	HMEC	breast
33	chr7:4764200-4765800	Flanking Active TSS	HUVEC	blood vessel
34	chr7:4764200-4766000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:4764200-4766000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:4764200-4766000	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr7:4764200-4766000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr7:4764200-4766000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr7:4764200-4766600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr7:4764400-4765200	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr7:4764400-4765200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr7:4764400-4765400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr7:4764400-4765600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr7:4764400-4765600	Active TSS	Aorta	Aorta
45	chr7:4764400-4765600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr7:4764400-4765600	Flanking Active TSS	Fetal Brain Female	brain
47	chr7:4764400-4765600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
48	chr7:4764400-4765600	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr7:4764400-4765600	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr7:4764400-4765600	Flanking Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links