Variant report

Variant	rs774246
Chromosome Location	chr7:26990816-26990817
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	chr7:26988409..26991338-chr7:26991544..26993555,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10081212	0.83[ASN][1000 genomes]
rs10242380	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257437	0.93[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10257464	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259208	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267689	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082312	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082315	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974418	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977871	0.81[CEU][hapmap]
rs13221446	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17500459	1.00[ASN][1000 genomes]
rs1874924	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs213515	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213516	0.94[CEU][hapmap]
rs213518	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213521	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213533	0.94[CEU][hapmap]
rs213536	0.94[CEU][hapmap]
rs2140998	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693661	0.81[CEU][hapmap]
rs2936423	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889704	1.00[ASN][1000 genomes]
rs477924	0.94[CEU][hapmap]
rs591895	0.94[CEU][hapmap]
rs6461982	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs659131	0.93[CEU][hapmap]
rs6974705	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs774247	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774252	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774253	0.81[CEU][hapmap]
rs774257	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774258	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774259	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774260	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774261	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774262	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774268	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776505	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7791056	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797624	1.00[ASN][1000 genomes]
rs7809419	1.00[JPT][hapmap]
rs954051	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1033272	chr7:26976426-27020206	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs774246	STK31	cis	cerebellum	SCAN
rs774246	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26985200-26994600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:26986800-26992000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr7:26987600-26992400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr7:26989000-26991400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:26989000-26992000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr7:26989400-26991600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr7:26989400-26992400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr7:26989600-26991000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:26989600-26991600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr7:26989600-26993000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:26990400-26991000	Active TSS	Fetal Lung	lung
12	chr7:26990600-26991200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr7:26990600-26991200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:26990600-26991200	Enhancers	NHDF-Ad	bronchial
15	chr7:26990800-26991600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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