Variant report

Variant	rs11634290
Chromosome Location	chr15:75984095-75984096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11072556	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1127646	0.94[ASN][1000 genomes]
rs1127648	0.89[GIH][hapmap];0.80[TSI][hapmap]
rs1127649	0.93[ASN][1000 genomes]
rs11636280	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12898809	0.91[GIH][hapmap];0.80[TSI][hapmap]
rs12900539	0.82[AFR][1000 genomes]
rs12905062	0.92[JPT][hapmap]
rs12913388	0.85[ASN][1000 genomes]
rs1964473	0.92[JPT][hapmap]
rs2017312	0.92[JPT][hapmap]
rs34175377	0.91[ASN][1000 genomes]
rs34611707	0.92[JPT][hapmap]
rs35839559	0.81[ASN][1000 genomes]
rs3751536	0.92[JPT][hapmap]
rs4414463	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs4503758	0.92[JPT][hapmap]
rs4592617	0.91[GIH][hapmap];0.80[TSI][hapmap]
rs4616261	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4886732	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181595	0.81[JPT][hapmap]
rs7182902	0.92[ASN][1000 genomes]
rs8023621	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs8026234	0.90[JPT][hapmap]
rs8027311	0.90[JPT][hapmap]
rs8028002	0.92[JPT][hapmap]
rs8030131	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8034760	0.89[GIH][hapmap];0.80[TSI][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11634290	PTPN9	cis	cerebellum	SCAN
rs11634290	RAB3GAP2	trans	parietal	SCAN
rs11634290	ETFA	cis	parietal	SCAN
rs11634290	SCAMP5	cis	parietal	SCAN
rs11634290	NRG4	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	chr15:75968800-75985600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:75969200-75985800	Weak transcription	Right Atrium	heart
12	chr15:75969600-75987600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:75970000-75985800	Weak transcription	Esophagus	oesophagus
14	chr15:75970600-75985800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:75973000-75985600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:75976000-75986000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:75976000-75986000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:75976200-75985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:75976200-75985800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:75976200-75985800	Weak transcription	Colonic Mucosa	Colon
21	chr15:75976200-75986000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:75976600-75984400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:75976800-75985600	Weak transcription	Ovary	ovary
24	chr15:75977200-75986000	Weak transcription	Fetal Intestine Large	intestine
25	chr15:75978800-75985600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:75979400-75985000	Strong transcription	Adipose Nuclei	Adipose
27	chr15:75979600-75984400	Strong transcription	Aorta	Aorta
28	chr15:75979600-75984600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:75979600-75984600	Strong transcription	Fetal Lung	lung
30	chr15:75979600-75985000	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:75979800-75984800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:75979800-75985600	Weak transcription	HMEC	breast
33	chr15:75980000-75985600	Strong transcription	Colon Smooth Muscle	Colon
34	chr15:75980200-75985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:75980400-75985600	Weak transcription	Lung	lung
36	chr15:75980600-75984800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:75980600-75984800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr15:75980800-75985600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:75981000-75984200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:75981000-75985000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:75981000-75986000	Weak transcription	Brain Substantia Nigra	brain
42	chr15:75981200-75985600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:75981400-75985600	Weak transcription	Right Ventricle	heart
44	chr15:75981400-75985800	Weak transcription	Spleen	Spleen
45	chr15:75981400-75986000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:75981600-75985600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:75981600-75985800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:75982200-75985800	Weak transcription	Gastric	stomach
49	chr15:75983000-75984200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:75983200-75985000	Strong transcription	Fetal Muscle Trunk	muscle

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