Variant report

Variant	rs11633539
Chromosome Location	chr15:75066296-75066297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75063283..75067975-chr15:75109233..75113882,6	MCF-7	breast:
2	chr15:75062956..75068550-chr15:75133333..75136759,7	MCF-7	breast:
3	chr15:75053056..75055399-chr15:75065687..75067958,2	K562	blood:
4	chr15:75065072..75069457-chr15:75091713..75095477,3	MCF-7	breast:
5	chr15:75065380..75067175-chr15:75075106..75076815,2	K562	blood:
6	chr15:75051136..75052999-chr15:75065266..75067915,2	K562	blood:

Variant related genes	Relation type
ENSG00000140506	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11553760	0.80[EUR][1000 genomes]
rs11553762	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631294	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631682	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]
rs11631689	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631817	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632547	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11632706	0.93[ASN][1000 genomes]
rs11632814	0.93[ASN][1000 genomes]
rs11632822	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633861	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11636256	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637637	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16970170	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs16972511	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16972853	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16973048	1.00[YRI][hapmap]
rs16973078	0.85[CHD][hapmap]
rs17861124	0.93[ASN][1000 genomes]
rs17861125	0.93[ASN][1000 genomes]
rs17861130	0.90[ASN][1000 genomes]
rs17861138	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17861139	0.93[ASN][1000 genomes]
rs17861141	0.90[ASN][1000 genomes]
rs17861142	0.93[ASN][1000 genomes]
rs17861145	0.93[ASN][1000 genomes]
rs2069519	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2069521	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069522	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2069524	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2069525	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2069526	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35197434	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35331038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35408600	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35603757	1.00[AFR][1000 genomes]
rs35738366	1.00[AFR][1000 genomes]
rs4646425	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646427	0.82[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56066141	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56748048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59902765	0.90[ASN][1000 genomes]
rs61671857	0.85[AFR][1000 genomes]
rs74025837	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74025839	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74025842	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74025843	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74025847	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74025850	0.85[AFR][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
rs11633539	SCAMP5	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75056000-75069000	Weak transcription	Lung	lung
2	chr15:75061400-75069000	Weak transcription	Liver	Liver
3	chr15:75062800-75069200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr15:75063000-75066800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:75063200-75066800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:75063200-75066800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:75063200-75066800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:75063200-75067400	Enhancers	Primary B cells from cord blood	blood
9	chr15:75063200-75069400	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:75063200-75069400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:75063400-75067600	Weak transcription	Spleen	Spleen
12	chr15:75063400-75068000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr15:75063400-75069400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr15:75063600-75067800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:75063600-75069000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr15:75063800-75067600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:75063800-75069000	Weak transcription	Fetal Heart	heart
18	chr15:75063800-75069000	Weak transcription	Right Atrium	heart
19	chr15:75064000-75066400	Enhancers	Colonic Mucosa	Colon
20	chr15:75064000-75069400	Weak transcription	Fetal Brain Male	brain
21	chr15:75064200-75066600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr15:75064200-75067400	Weak transcription	Thymus	Thymus
23	chr15:75064400-75066400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:75064400-75068000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:75064400-75069000	Weak transcription	HUVEC	blood vessel
26	chr15:75064400-75069400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:75064400-75069400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:75064400-75069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:75064600-75067000	Enhancers	Brain Hippocampus Middle	brain
30	chr15:75064600-75067600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:75064600-75068200	Weak transcription	Dnd41	blood
32	chr15:75064600-75069200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:75065000-75067600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr15:75065200-75066400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr15:75065200-75066600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr15:75065200-75066800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:75065400-75066400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr15:75065400-75066600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr15:75065400-75066600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr15:75065400-75067000	Enhancers	Stomach Mucosa	stomach
41	chr15:75065400-75067200	Enhancers	GM12878-XiMat	blood
42	chr15:75065400-75069000	Weak transcription	Brain Substantia Nigra	brain
43	chr15:75065400-75069200	Enhancers	Primary T cells from cord blood	blood
44	chr15:75065400-75069200	Enhancers	Duodenum Mucosa	Duodenum
45	chr15:75065600-75066400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr15:75065600-75066400	Enhancers	Small Intestine	intestine
47	chr15:75065600-75066400	Flanking Active TSS	HepG2	liver
48	chr15:75065600-75066600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:75065600-75066800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr15:75065600-75066800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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