Variant report

Variant	rs1105288
Chromosome Location	chr15:83441343-83441344
allele	C/G
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:

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

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1109373	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1112679	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11259947	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11259948	0.91[CHB][hapmap]
rs12907913	0.91[CHB][hapmap]
rs12913102	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1533136	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971555	0.82[CHB][hapmap]
rs4260027	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8028133	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028917	0.87[YRI][hapmap]
rs8033573	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1105288	MEX3B	cis	parietal	SCAN
rs1105288	RASGRF1	cis	cerebellum	SCAN
rs1105288	EFTUD1	cis	cerebellum	SCAN
rs1105288	WHAMM	cis	Adipose Subcutaneous	GTEx
rs1105288	BTBD1	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr15:83434400-83442000	Weak transcription	Pancreas	Pancrea
5	chr15:83434400-83443200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:83434600-83442000	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:83434600-83443200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:83434600-83446600	Weak transcription	Fetal Heart	heart
9	chr15:83434800-83443200	Weak transcription	Brain Angular Gyrus	brain
10	chr15:83434800-83443400	Weak transcription	Lung	lung
11	chr15:83434800-83462200	Weak transcription	Ovary	ovary
12	chr15:83435000-83442000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:83435000-83442200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:83435200-83442200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:83435200-83452600	Weak transcription	Fetal Brain Female	brain
16	chr15:83435200-83457000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:83435600-83443400	Strong transcription	Left Ventricle	heart
18	chr15:83436400-83467800	Weak transcription	Psoas Muscle	Psoas
19	chr15:83436600-83445200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:83436800-83441800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:83437000-83448400	Weak transcription	Fetal Stomach	stomach
22	chr15:83437600-83442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:83437800-83453200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:83438000-83441400	Weak transcription	HSMM	muscle
25	chr15:83439800-83441400	Strong transcription	Fetal Muscle Leg	muscle
26	chr15:83439800-83441400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:83440200-83441400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:83440800-83468000	Weak transcription	Right Ventricle	heart
29	chr15:83441000-83441400	Enhancers	K562	blood
30	chr15:83441000-83443400	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:83441200-83441400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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