Variant report

Variant	rs1105287
Chromosome Location	chr15:83441012-83441013
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83438498..83441390-chr15:83475483..83477867,2	K562	blood:
2	chr15:83432102..83434403-chr15:83439416..83441912,2	MCF-7	breast:
3	chr15:83417627..83419593-chr15:83440111..83442179,2	MCF-7	breast:
4	chr15:83315100..83318096-chr15:83438505..83441476,2	K562	blood:
5	chr15:83438774..83441165-chr15:83453782..83456653,2	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction
ENSG00000259462	Chromatin interaction
ENSG00000214575	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11631033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11631209	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11631378	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633676	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11635290	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11635357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11637448	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637563	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11857233	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1256430	0.82[GIH][hapmap]
rs12907810	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12914752	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs12917248	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1553886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2137052	0.90[EUR][1000 genomes]
rs34337936	0.88[EUR][1000 genomes]
rs35590674	0.90[EUR][1000 genomes]
rs35852340	0.91[EUR][1000 genomes]
rs35989107	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35989256	0.90[EUR][1000 genomes]
rs3814281	0.95[GIH][hapmap];0.85[TSI][hapmap]
rs4132210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4779061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57252413	0.84[EUR][1000 genomes]
rs60414706	0.84[EUR][1000 genomes]
rs72753973	0.91[EUR][1000 genomes]
rs9806642	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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	45 gene(s)	inside rSNPs	diseases
11	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	esv3346074	chr15:83422947-83456222	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1105287	RASGRF1	cis	cerebellum	SCAN
rs1105287	PSMA4	cis	parietal	SCAN
rs1105287	FAM154B	cis	parietal	SCAN
rs1105287	WHAMM	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83425000-83447800	Weak transcription	Fetal Brain Male	brain
2	chr15:83427800-83442200	Weak transcription	Brain Substantia Nigra	brain
3	chr15:83428000-83442200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:83434200-83441200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:83434400-83442000	Weak transcription	Pancreas	Pancrea
6	chr15:83434400-83443200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr15:83434600-83442000	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:83434600-83443200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:83434600-83446600	Weak transcription	Fetal Heart	heart
10	chr15:83434800-83443200	Weak transcription	Brain Angular Gyrus	brain
11	chr15:83434800-83443400	Weak transcription	Lung	lung
12	chr15:83434800-83462200	Weak transcription	Ovary	ovary
13	chr15:83435000-83442000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:83435000-83442200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:83435200-83442200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:83435200-83452600	Weak transcription	Fetal Brain Female	brain
17	chr15:83435200-83457000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:83435600-83443400	Strong transcription	Left Ventricle	heart
19	chr15:83436400-83467800	Weak transcription	Psoas Muscle	Psoas
20	chr15:83436600-83445200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:83436800-83441800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:83437000-83448400	Weak transcription	Fetal Stomach	stomach
23	chr15:83437600-83442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:83437800-83453200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:83438000-83441400	Weak transcription	HSMM	muscle
26	chr15:83439600-83441200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:83439600-83441200	Enhancers	HMEC	breast
28	chr15:83439800-83441400	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:83439800-83441400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr15:83440200-83441200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:83440200-83441400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:83440800-83468000	Weak transcription	Right Ventricle	heart
33	chr15:83441000-83441400	Enhancers	K562	blood
34	chr15:83441000-83443400	Strong transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links