Variant report

Variant	rs11070356
Chromosome Location	chr15:42338695-42338696
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	chr15:42326859..42328863-chr15:42337249..42339114,2	MCF-7	breast:
2	chr15:42334601..42336170-chr15:42337755..42339469,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12148273	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17690109	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17690827	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17690899	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17691153	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17747505	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17748059	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs17748132	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap]
rs1993069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412656	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28568280	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3743017	1.00[ASW][hapmap]
rs4923922	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4923923	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4923924	0.87[EUR][1000 genomes]
rs4923925	0.87[EUR][1000 genomes]
rs4923928	0.92[CEU][hapmap]
rs4924608	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4924609	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924611	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924614	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924615	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924616	0.87[EUR][1000 genomes]
rs4924617	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924620	0.92[CEU][hapmap];1.00[GIH][hapmap]
rs7162019	0.92[CEU][hapmap]
rs7165460	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs7166026	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166111	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166789	0.92[CEU][hapmap]
rs7168863	0.91[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173686	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7176443	1.00[CEU][hapmap]
rs7177034	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180420	0.87[EUR][1000 genomes]
rs750051	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs750052	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs755599	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8029713	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11070356	GPR176	cis	cerebellum	SCAN
rs11070356	RTF1	cis	parietal	SCAN
rs11070356	MEIS2	cis	parietal	SCAN
rs11070356	IVD	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42330200-42339600	Weak transcription	Lung	lung
2	chr15:42331000-42341000	Weak transcription	Esophagus	oesophagus
3	chr15:42333000-42341000	Weak transcription	Right Atrium	heart
4	chr15:42335600-42340600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42336400-42339600	Enhancers	Pancreas	Pancrea
6	chr15:42337200-42339200	Enhancers	K562	blood
7	chr15:42337400-42340400	Weak transcription	NHEK	skin
8	chr15:42337600-42338800	Bivalent Enhancer	HepG2	liver
9	chr15:42337600-42339600	Enhancers	A549	lung
10	chr15:42337800-42340200	Weak transcription	Placenta	Placenta
11	chr15:42337800-42340800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:42337800-42340800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:42337800-42341600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:42338400-42338800	Enhancers	Gastric	stomach
15	chr15:42338400-42339600	Enhancers	Fetal Intestine Large	intestine
16	chr15:42338400-42340800	Weak transcription	Fetal Muscle Leg	muscle

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