Variant report

Variant	rs4414463
Chromosome Location	chr15:75980112-75980113
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	chr15:75978548..75980308-chr15:76018385..76020892,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1127646	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1127648	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631648	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11634290	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs11634497	0.86[EUR][1000 genomes]
rs11636221	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11636280	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11636352	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12898809	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900539	0.91[EUR][1000 genomes]
rs4592617	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886732	0.87[ASN][1000 genomes]
rs7182902	0.88[EUR][1000 genomes]
rs8027239	0.87[EUR][1000 genomes]
rs8030131	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034760	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
6	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
7	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
9	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
11	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv904395	chr15:75957928-75984095	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
14	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
15	nsv569997	chr15:75965169-75991451	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
16	nsv984092	chr15:75970252-76000687	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4414463	PTPN9	cis	cerebellum	SCAN
rs4414463	SCAMP5	cis	parietal	SCAN
rs4414463	ETFA	cis	parietal	SCAN
rs4414463	CSPG4	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75965800-75986000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:75966400-75993200	Weak transcription	Hela-S3	cervix
3	chr15:75966600-75986000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:75966800-75985600	Weak transcription	Osteobl	bone
5	chr15:75968000-75985600	Strong transcription	Fetal Stomach	stomach
6	chr15:75968200-75985800	Weak transcription	Left Ventricle	heart
7	chr15:75968400-75984600	Strong transcription	NHLF	lung
8	chr15:75968400-75985000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:75968400-75985600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:75968800-75980400	Weak transcription	Brain Substantia Nigra	brain
11	chr15:75968800-75985600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:75969200-75985800	Weak transcription	Right Atrium	heart
13	chr15:75969600-75987600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:75970000-75980400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:75970000-75985800	Weak transcription	Esophagus	oesophagus
16	chr15:75970600-75985800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:75973000-75985600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:75976000-75986000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:75976000-75986000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:75976200-75985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:75976200-75985800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:75976200-75985800	Weak transcription	Colonic Mucosa	Colon
23	chr15:75976200-75986000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:75976600-75984400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:75976800-75980200	Weak transcription	Fetal Intestine Small	intestine
26	chr15:75976800-75985600	Weak transcription	Ovary	ovary
27	chr15:75977200-75983800	Weak transcription	NH-A	brain
28	chr15:75977200-75986000	Weak transcription	Fetal Intestine Large	intestine
29	chr15:75977600-75980400	Weak transcription	Placenta	Placenta
30	chr15:75978400-75980600	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr15:75978600-75980200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:75978800-75985600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr15:75979000-75980600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:75979000-75981000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:75979000-75984000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:75979400-75981000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:75979400-75981600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:75979400-75982200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:75979400-75985000	Strong transcription	Adipose Nuclei	Adipose
40	chr15:75979600-75981000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:75979600-75981400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:75979600-75981800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:75979600-75982000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:75979600-75982200	Strong transcription	NHDF-Ad	bronchial
45	chr15:75979600-75983200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:75979600-75984400	Strong transcription	Aorta	Aorta
47	chr15:75979600-75984600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:75979600-75984600	Strong transcription	Fetal Lung	lung
49	chr15:75979600-75985000	Strong transcription	Fetal Muscle Leg	muscle
50	chr15:75979800-75980800	Strong transcription	Rectal Smooth Muscle	rectum

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