Variant report

Variant	rs3173628
Chromosome Location	chr7:12627245-12627246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12620852..12624352-chr7:12625661..12628427,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWDE-7	chr7:12626246-12628008	NONHSAT119236

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10233337	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10248988	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10255606	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10276226	0.92[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1129315	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17283514	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17283696	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1859989	0.92[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1859990	0.92[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1990223	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1990224	0.95[JPT][hapmap];0.87[MEX][hapmap]
rs1990225	0.95[JPT][hapmap];0.87[MEX][hapmap]
rs2215063	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2240571	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2240574	0.96[CEU][hapmap]
rs2240575	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3735221	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807863	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41379149	0.92[CEU][hapmap]
rs4361677	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460965	0.92[CEU][hapmap]
rs6460967	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6460968	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6954111	0.92[CEU][hapmap]
rs6954578	0.92[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs6972477	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73293093	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7801351	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7811582	0.96[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs968792	0.85[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3173628	SCIN	cis	parietal	SCAN
rs3173628	SOSTDC1	cis	cerebellum	SCAN
rs3173628	SCIN	cis	Thyroid	GTEx
rs3173628	SCIN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12611800-12637600	Weak transcription	Colonic Mucosa	Colon
2	chr7:12619800-12630400	Weak transcription	Esophagus	oesophagus
3	chr7:12623400-12628000	Weak transcription	Placenta	Placenta
4	chr7:12625000-12627800	Enhancers	K562	blood
5	chr7:12625000-12645800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:12625000-12652000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:12625200-12627400	Weak transcription	Stomach Mucosa	stomach
8	chr7:12625400-12667600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:12625600-12633400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:12625800-12628000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:12626000-12628600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:12626200-12637400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:12627000-12627400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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