Variant report

Variant	rs11857695
Chromosome Location	chr15:75165751-75165752
allele	G/T
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	JUND	chr15:75165447-75165888	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:75165238-75166050	HUVEC	blood vessel:	n/a	n/a
3	EBF1	chr15:75165317-75165764	GM12878	blood:	n/a	chr15:75165493-75165504
4	MAX	chr15:75165075-75165887	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr15:75164765-75165761	GM12878	blood:	n/a	n/a
6	PBX3	chr15:75165095-75166185	SK-N-SH	brain:	n/a	chr15:75165424-75165444
7	TBP	chr15:75165161-75166216	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:75165238-75165938	Gliobla	brain:	n/a	n/a
9	MAZ	chr15:75165284-75165909	HepG2	liver:	n/a	n/a
10	ELF1	chr15:75165196-75165946	SK-N-SH	brain:	n/a	chr15:75165680-75165691 chr15:75165681-75165690 chr15:75165680-75165691
11	REST	chr15:75165164-75165776	A549	lung:	n/a	chr15:75165335-75165345
12	YY1	chr15:75165308-75165943	HepG2	liver:	n/a	chr15:75165481-75165490
13	ELF1	chr15:75165310-75165941	K562	blood:	n/a	chr15:75165680-75165691 chr15:75165681-75165690 chr15:75165680-75165691
14	POLR2A	chr15:75165115-75165818	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr15:75165079-75165767	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:75165085-75165996	H1-neurons	neurons:	n/a	n/a
17	MAX	chr15:75165119-75166288	H1-hESC	embryonic stem cell:	n/a	n/a
18	NRF1	chr15:75165517-75165891	H1-hESC	embryonic stem cell:	n/a	chr15:75165707-75165721 chr15:75165706-75165717 chr15:75165707-75165718
19	SP1	chr15:75165023-75165894	H1-hESC	embryonic stem cell:	n/a	chr15:75165438-75165449 chr15:75165731-75165741 chr15:75165410-75165431 chr15:75165731-75165741 chr15:75165339-75165348 chr15:75165338-75165350 chr15:75165338-75165350 chr15:75165340-75165349 chr15:75165339-75165353
20	POLR2A	chr15:75165066-75166210	ECC-1	luminal epithelium:	n/a	n/a
21	ELK1	chr15:75165227-75166103	K562	blood:	n/a	n/a
22	CREB1	chr15:75165253-75165791	A549	lung:	n/a	n/a
23	MAX	chr15:75164982-75166402	K562	blood:	n/a	n/a
24	POLR2A	chr15:75164803-75166025	GM19193	blood:	n/a	n/a
25	TAF1	chr15:75165402-75165811	SK-N-SH	brain:	n/a	n/a
26	ATF2	chr15:75164927-75166133	GM12878	blood:	n/a	n/a
27	EGR1	chr15:75165559-75165963	K562	blood:	n/a	chr15:75165708-75165717 chr15:75165680-75165689
28	POLR2A	chr15:75165096-75166029	HepG2	liver:	n/a	n/a
29	GABPA	chr15:75165171-75165929	K562	blood:	n/a	chr15:75165707-75165721 chr15:75165707-75165718
30	RCOR1	chr15:75165209-75165754	HepG2	liver:	n/a	n/a
31	TAF1	chr15:75165543-75165752	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr15:75165212-75166051	SK-N-SH	brain:	n/a	n/a
33	RELA	chr15:75165100-75166040	GM19099	blood:	n/a	n/a
34	ELF1	chr15:75165033-75166320	MCF-7	breast:	n/a	chr15:75165680-75165691 chr15:75165681-75165690 chr15:75165680-75165691
35	CREB1	chr15:75165213-75166267	A549	lung:	n/a	n/a
36	POLR2A	chr15:75165126-75166324	PFSK-1	brain:	n/a	n/a
37	CHD2	chr15:75165196-75165775	Hela-S3	cervix:	n/a	n/a
38	ZBTB7A	chr15:75165071-75166161	ECC-1	luminal epithelium:	n/a	n/a
39	ZNF143	chr15:75165353-75165815	Hela-S3	cervix:	n/a	chr15:75165478-75165488
40	CHD2	chr15:75165142-75165990	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr15:75165258-75166016	K562	blood:	n/a	n/a
42	MAX	chr15:75165180-75165902	ECC-1	luminal epithelium:	n/a	n/a
43	MAX	chr15:75165107-75166094	ECC-1	luminal epithelium:	n/a	n/a
44	CREB1	chr15:75165027-75166253	HepG2	liver:	n/a	n/a
45	POLR2A	chr15:75165045-75165957	HL-60	blood:	n/a	n/a
46	POLR2A	chr15:75165133-75166017	GM18951	blood:	n/a	n/a
47	TCF3	chr15:75165202-75165860	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:75165144-75166371	K562	blood:	n/a	n/a
49	ELF1	chr15:75165243-75165875	A549	lung:	n/a	chr15:75165680-75165691 chr15:75165681-75165690 chr15:75165680-75165691
50	PBX3	chr15:75165131-75165769	A549	lung:	n/a	chr15:75165424-75165444

No.	Distal block	Cell Line	Cell type
1	chr15:75163746..75165751-chr15:75191304..75195509,4	K562	blood:
2	chr15:75132063..75136088-chr15:75165447..75167881,5	K562	blood:
3	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
4	chr15:75164429..75167842-chr15:75196018..75198435,3	K562	blood:
5	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:
6	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
7	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
8	chr15:75163895..75166026-chr15:75315159..75317542,2	MCF-7	breast:
9	chr15:75073135..75075746-chr15:75163972..75165852,2	K562	blood:
10	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
11	chr15:75110223..75112810-chr15:75165268..75167627,2	MCF-7	breast:
12	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
13	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
14	chr15:75164573..75166914-chr15:75228746..75230664,2	K562	blood:

Variant related genes	Relation type
SCAMP2	TF binding region
ENSG00000140506	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000178741	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11072511	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072512	0.93[EUR][1000 genomes]
rs11072513	0.81[EUR][1000 genomes]
rs11072514	0.84[EUR][1000 genomes]
rs1127796	0.94[EUR][1000 genomes]
rs1130741	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1133322	0.90[EUR][1000 genomes]
rs1133323	0.83[EUR][1000 genomes]
rs11630918	0.89[EUR][1000 genomes]
rs11633472	0.87[EUR][1000 genomes]
rs11638130	0.86[EUR][1000 genomes]
rs11854704	0.88[EUR][1000 genomes]
rs11856413	0.86[EUR][1000 genomes]
rs12441499	0.83[AFR][1000 genomes]
rs12898539	0.85[EUR][1000 genomes]
rs12899430	0.85[EUR][1000 genomes]
rs12899787	0.90[EUR][1000 genomes]
rs12900662	0.97[EUR][1000 genomes]
rs12901190	0.83[EUR][1000 genomes]
rs12902515	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903205	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12903370	0.84[EUR][1000 genomes]
rs12904326	0.83[EUR][1000 genomes]
rs12904897	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907898	0.92[EUR][1000 genomes]
rs12908365	0.90[EUR][1000 genomes]
rs12909335	0.83[EUR][1000 genomes]
rs12911254	0.91[EUR][1000 genomes]
rs12912839	0.84[EUR][1000 genomes]
rs12913293	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12914217	0.81[EUR][1000 genomes]
rs2044157	0.81[EUR][1000 genomes]
rs3935818	0.82[AFR][1000 genomes]
rs4643278	0.98[EUR][1000 genomes]
rs4886608	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886632	0.98[EUR][1000 genomes]
rs4886636	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886639	0.85[EUR][1000 genomes]
rs56671860	0.83[AFR][1000 genomes]
rs59945415	0.91[EUR][1000 genomes]
rs60494786	0.83[AFR][1000 genomes]
rs62029167	0.91[EUR][1000 genomes]
rs7179093	0.82[AFR][1000 genomes]
rs729263	0.83[AFR][1000 genomes]
rs7495664	0.84[EUR][1000 genomes]
rs7495739	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7497026	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7497393	0.90[EUR][1000 genomes]
rs8025447	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv827386	chr15:75161362-75166473	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
4	nsv827388	chr15:75161362-75169121	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11857695	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs11857695	SCAMP2	cis	Esophagus Mucosa	GTEx
rs11857695	ULK3	cis	Whole Blood	GTEx
rs11857695	SCAMP5	cis	Artery Tibial	GTEx
rs11857695	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs11857695	SCAMP2	cis	Whole Blood	GTEx
rs11857695	MPI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75163800-75166000	Active TSS	GM12878-XiMat	blood
2	chr15:75164200-75166000	Active TSS	Stomach Smooth Muscle	stomach
3	chr15:75164200-75166400	Active TSS	Rectal Smooth Muscle	rectum
4	chr15:75164400-75166400	Active TSS	HSMMtube	muscle
5	chr15:75164600-75165800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:75164600-75165800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:75164600-75165800	Active TSS	HMEC	breast
8	chr15:75164600-75165800	Active TSS	HSMM	muscle
9	chr15:75164600-75166000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:75164600-75166000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr15:75164600-75166000	Active TSS	Gastric	stomach
12	chr15:75164600-75166000	Active TSS	NHLF	lung
13	chr15:75164600-75166200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr15:75164600-75166200	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr15:75164600-75166400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:75164600-75166400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:75164600-75166400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr15:75164600-75166400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:75164600-75166400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr15:75164600-75166400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr15:75164600-75166400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:75164600-75166400	Active TSS	Brain Cingulate Gyrus	brain
23	chr15:75164600-75166400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr15:75164600-75166400	Active TSS	A549	lung
25	chr15:75164600-75166600	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr15:75164800-75166000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:75164800-75166000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:75164800-75166000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:75164800-75166000	Active TSS	Primary T cells from cord blood	blood
30	chr15:75164800-75166000	Active TSS	Brain Angular Gyrus	brain
31	chr15:75164800-75166000	Active TSS	Lung	lung
32	chr15:75164800-75166000	Active TSS	Ovary	ovary
33	chr15:75164800-75166000	Active TSS	Small Intestine	intestine
34	chr15:75164800-75166200	Active TSS	Aorta	Aorta
35	chr15:75164800-75166200	Active TSS	Esophagus	oesophagus
36	chr15:75164800-75166200	Active TSS	Left Ventricle	heart
37	chr15:75164800-75166200	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr15:75164800-75166400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr15:75164800-75166400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr15:75164800-75166400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr15:75164800-75166400	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr15:75164800-75166400	Active TSS	Stomach Mucosa	stomach
43	chr15:75164800-75166400	Active TSS	NHDF-Ad	bronchial
44	chr15:75165000-75166000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:75165000-75166000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:75165000-75166000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:75165000-75166000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:75165000-75166000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:75165000-75166000	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr15:75165000-75166000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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