Variant report

Variant	rs2723520
Chromosome Location	chr7:17813677-17813678
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	chr7:17811330..17814025-chr7:17979627..17981525,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDAC9-11	chr7:17812631-17814939	NONHSAT119344

Variant related genes	Relation type
ENSG00000071189	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10249221	0.91[ASN][1000 genomes]
rs10264355	1.00[ASN][1000 genomes]
rs10264445	0.91[ASN][1000 genomes]
rs10264447	0.91[ASN][1000 genomes]
rs1357796	0.81[YRI][hapmap]
rs1404416	1.00[ASN][1000 genomes]
rs1404417	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404418	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404419	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404421	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1404422	0.84[MKK][hapmap]
rs1404425	0.94[ASN][1000 genomes]
rs1830006	0.94[ASN][1000 genomes]
rs1965534	0.96[ASN][1000 genomes]
rs1997019	0.94[ASN][1000 genomes]
rs2068172	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110015	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254361	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254594	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254737	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs2537592	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537593	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537594	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691556	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2691581	0.96[ASN][1000 genomes]
rs2691582	0.96[ASN][1000 genomes]
rs2691584	1.00[ASN][1000 genomes]
rs2691592	1.00[ASN][1000 genomes]
rs2691593	1.00[ASN][1000 genomes]
rs2691595	1.00[ASN][1000 genomes]
rs2691596	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2691604	1.00[ASN][1000 genomes]
rs2691610	1.00[ASN][1000 genomes]
rs2691616	1.00[ASN][1000 genomes]
rs2691617	1.00[ASN][1000 genomes]
rs2723503	1.00[ASN][1000 genomes]
rs2723506	1.00[ASN][1000 genomes]
rs2723507	1.00[ASN][1000 genomes]
rs2723508	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2723509	1.00[ASN][1000 genomes]
rs2723510	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2723511	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2723513	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723514	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723516	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723518	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723519	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4316058	0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4721666	0.82[YRI][hapmap]
rs949451	0.86[MKK][hapmap]

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	nsv869352	chr7:17237983-17932878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1021289	chr7:17254117-17873816	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv538754	chr7:17254117-17873816	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv534309	chr7:17254118-17932878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv887804	chr7:17571140-17885468	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
10	esv2764016	chr7:17800816-17815402	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv12823	chr7:17813669-17814724	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2723520	SOSTDC1	cis	cerebellum	SCAN
rs2723520	AHR	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17809200-17813800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr7:17810200-17815000	Enhancers	HMEC	breast
3	chr7:17811600-17813800	Enhancers	Fetal Thymus	thymus
4	chr7:17811800-17814200	Enhancers	Right Ventricle	heart
5	chr7:17812000-17813800	Enhancers	HSMM	muscle
6	chr7:17812000-17814200	Enhancers	Left Ventricle	heart
7	chr7:17812000-17814400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:17812000-17814400	Enhancers	NHLF	lung
9	chr7:17812000-17814600	Enhancers	NHDF-Ad	bronchial
10	chr7:17812000-17815000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:17812000-17815200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:17812200-17813800	Enhancers	Hela-S3	cervix
13	chr7:17812200-17813800	Enhancers	NHEK	skin
14	chr7:17812200-17814600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:17812200-17815200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:17812200-17815400	Enhancers	NH-A	brain
17	chr7:17812400-17814400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:17812400-17814600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:17812400-17815000	Enhancers	Osteobl	bone
20	chr7:17812400-17846200	Weak transcription	Fetal Stomach	stomach
21	chr7:17812400-17852200	Weak transcription	Esophagus	oesophagus
22	chr7:17812600-17813800	Weak transcription	Pancreas	Pancrea
23	chr7:17812600-17814600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:17812600-17887600	Weak transcription	Gastric	stomach
25	chr7:17812800-17813800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr7:17813000-17815000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:17813400-17813800	Flanking Active TSS	Fetal Heart	heart
28	chr7:17813400-17814800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:17813400-17814800	Weak transcription	Placenta	Placenta
30	chr7:17813400-17815000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:17813400-17821200	Weak transcription	Thymus	Thymus
32	chr7:17813600-17813800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr7:17813600-17879200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links