Variant report

Variant	rs3743135
Chromosome Location	chr15:40558482-40558483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:40558412-40559685	IMR90	lung:	n/a	n/a
2	POLR2A	chr15:40558211-40559183	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40556498..40560954-chr15:40561713..40567483,5	MCF-7	breast:

Variant related genes	Relation type
PAK6	TF binding region
ENSG00000137843	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1075505	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1075506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902461	0.95[ASN][1000 genomes]
rs2277564	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2412504	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743132	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162809	0.95[ASN][1000 genomes]
rs8037267	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs936216	0.88[JPT][hapmap]
rs936217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv904097	chr15:40555065-40595627	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv517541	chr15:40557268-40595627	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40546000-40558600	Weak transcription	Brain Angular Gyrus	brain
2	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
3	chr15:40546200-40568200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:40546800-40559200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:40550000-40568000	Weak transcription	Spleen	Spleen
6	chr15:40550400-40566800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40551200-40558800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:40551400-40558800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:40551400-40561600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:40551400-40571000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:40551600-40558600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:40551600-40560000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:40551600-40561800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:40553800-40570400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:40554800-40559000	Enhancers	Hela-S3	cervix
16	chr15:40554800-40559200	Weak transcription	Fetal Brain Female	brain
17	chr15:40555000-40560600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:40555200-40558600	Strong transcription	Esophagus	oesophagus
19	chr15:40555400-40566600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:40555600-40558800	Weak transcription	HSMMtube	muscle
21	chr15:40555800-40558600	Weak transcription	HSMM	muscle
22	chr15:40555800-40558600	Weak transcription	NH-A	brain
23	chr15:40555800-40558600	Weak transcription	NHDF-Ad	bronchial
24	chr15:40555800-40558800	Weak transcription	Osteobl	bone
25	chr15:40556000-40558600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:40556000-40558800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:40556000-40558800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:40556200-40567400	Strong transcription	Fetal Intestine Small	intestine
29	chr15:40556200-40567600	Weak transcription	Colonic Mucosa	Colon
30	chr15:40556800-40558800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:40557000-40559800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr15:40557000-40568200	Weak transcription	Lung	lung
33	chr15:40557200-40558800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:40557200-40562000	Strong transcription	Fetal Intestine Large	intestine
35	chr15:40557200-40571800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:40557400-40558600	Weak transcription	Ovary	ovary
37	chr15:40557400-40558800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:40557400-40566800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:40557600-40558600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:40557600-40558600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:40557600-40560200	Enhancers	A549	lung
42	chr15:40557600-40561000	Strong transcription	Pancreas	Pancrea
43	chr15:40557800-40559800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:40558000-40559000	Strong transcription	Gastric	stomach
45	chr15:40558000-40559600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:40558000-40559600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:40558200-40558600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:40558200-40558600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:40558200-40559400	Genic enhancers	Placenta	Placenta
50	chr15:40558200-40559600	Enhancers	Placenta Amnion	Placenta Amnion

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