Variant report

Variant	rs10232563
Chromosome Location	chr7:4881140-4881141
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	chr7:4877219..4880188-chr7:4880531..4883459,5	K562	blood:
2	chr7:4879131..4881238-chr7:4883956..4886744,2	K562	blood:

Variant related genes	Relation type
ENSG00000157927	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10225766	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11982597	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13243520	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3763381	0.91[MEX][hapmap]
rs4720427	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs6958275	0.87[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6958439	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6964780	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6966725	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6969146	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6976105	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7776704	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7799814	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
4	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
5	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
6	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
7	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
8	nsv823994	chr7:4792385-4928328	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv528748	chr7:4820581-5010993	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029123	chr7:4821734-4919277	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1021170	chr7:4831361-5058033	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv538706	chr7:4831361-5058033	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1025467	chr7:4850447-5021443	ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv605979	chr7:4854592-4944514	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1021999	chr7:4862082-5003190	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv538707	chr7:4862082-5003190	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv1033855	chr7:4862677-5069764	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv605980	chr7:4876057-5003373	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10232563	AMZ1	cis	parietal	SCAN
rs10232563	FTSJ2	cis	parietal	SCAN
rs10232563	ACTB	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4865000-4882000	Weak transcription	Ovary	ovary
2	chr7:4865000-4885200	Weak transcription	Brain Anterior Caudate	brain
3	chr7:4870200-4881200	Weak transcription	Spleen	Spleen
4	chr7:4876000-4881800	Weak transcription	Pancreas	Pancrea
5	chr7:4876200-4890400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:4877400-4882200	Weak transcription	Fetal Kidney	kidney
7	chr7:4878200-4885200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:4878200-4885400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:4878200-4885400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:4878400-4885400	Weak transcription	Right Atrium	heart
11	chr7:4878600-4881800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:4878600-4882000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:4878600-4883200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:4878600-4885400	Weak transcription	Right Ventricle	heart
15	chr7:4878800-4885400	Weak transcription	Fetal Brain Male	brain
16	chr7:4879600-4883200	Enhancers	Fetal Lung	lung
17	chr7:4880000-4884800	Weak transcription	Brain Germinal Matrix	brain
18	chr7:4880800-4881200	ZNF genes & repeats	Fetal Stomach	stomach
19	chr7:4880800-4882200	Bivalent Enhancer	Placenta	Placenta
20	chr7:4881000-4881200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr7:4881000-4881200	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links