Variant report

Variant	rs11631682
Chromosome Location	chr15:75056358-75056359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75052612..75054479-chr15:75056291..75058590,3	K562	blood:
2	chr15:75056268..75058478-chr15:75059962..75062462,2	K562	blood:
3	chr15:75042997..75044715-chr15:75054154..75056433,2	K562	blood:
4	chr15:75055933..75058709-chr15:75257513..75259358,2	K562	blood:
5	chr15:75056268..75058478-chr15:75059962..75062607,3	K562	blood:
6	chr15:74726274..74728760-chr15:75055542..75058469,2	K562	blood:

Variant related genes	Relation type
ENSG00000138623	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11553762	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs11631294	0.90[ASN][1000 genomes]
rs11631689	0.95[ASN][1000 genomes]
rs11631817	0.87[ASN][1000 genomes]
rs11632547	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632706	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11632814	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11632822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633539	0.82[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633861	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636256	0.95[ASN][1000 genomes]
rs11637637	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs16970078	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs16970170	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs16972511	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs16972853	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs16973048	0.89[YRI][hapmap]
rs16973078	0.85[CHD][hapmap];0.83[TSI][hapmap]
rs17861124	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17861125	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17861130	0.92[ASN][1000 genomes]
rs17861135	0.84[AFR][1000 genomes]
rs17861138	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17861139	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17861141	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17861142	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17861145	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069519	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2069522	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069525	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069526	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35197434	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35331038	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35408600	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35603757	0.90[AFR][1000 genomes]
rs35738366	0.90[AFR][1000 genomes]
rs4646425	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646427	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56066141	0.95[ASN][1000 genomes]
rs56748048	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59902765	0.87[ASN][1000 genomes]
rs74025837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025839	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025842	0.95[ASN][1000 genomes]
rs74025843	0.95[ASN][1000 genomes]
rs74025847	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers 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 miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11631682	SCAMP5	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75044800-75062600	Weak transcription	Right Atrium	heart
2	chr15:75047200-75063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:75053600-75056400	Enhancers	Fetal Intestine Small	intestine
4	chr15:75054000-75056400	Enhancers	Placenta	Placenta
5	chr15:75054200-75056400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr15:75054200-75057000	Enhancers	Fetal Muscle Trunk	muscle
7	chr15:75054600-75056400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:75054800-75056400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:75054800-75056400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:75054800-75060600	Weak transcription	HepG2	liver
11	chr15:75055000-75056400	Enhancers	NHEK	skin
12	chr15:75055200-75063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:75055400-75061000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:75055600-75060600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:75055600-75061000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:75055600-75061000	Weak transcription	HUVEC	blood vessel
17	chr15:75055600-75065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75056000-75056400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:75056000-75060800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:75056000-75061000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr15:75056000-75061000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:75056000-75061000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:75056000-75069000	Weak transcription	Lung	lung
24	chr15:75056200-75056400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:75056200-75056400	Enhancers	Duodenum Mucosa	Duodenum
26	chr15:75056200-75060400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:75056200-75061000	Weak transcription	HMEC	breast
28	chr15:75056200-75063200	Weak transcription	Spleen	Spleen

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