Variant report

Variant	rs7163390
Chromosome Location	chr15:75280426-75280427
allele	C/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	CTCF	chr15:75280395-75280682	HepG2	liver:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
2	CTCF	chr15:75280420-75280570	HFF-Myc	foreskin:	n/a	n/a
3	YY1	chr15:75280409-75280637	GM12891	blood:	n/a	n/a
4	SMC3	chr15:75280340-75280750	SK-N-SH	brain:	n/a	chr15:75280567-75280581
5	CTCF	chr15:75280290-75280966	A549	lung:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
6	RAD21	chr15:75280343-75280796	H1-hESC	embryonic stem cell:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
7	CTCF	chr15:75280320-75280927	HCT-116	colon:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
8	SMC3	chr15:75280393-75280731	K562	blood:	n/a	chr15:75280567-75280581
9	REST	chr15:75280336-75280654	SK-N-SH	brain:	n/a	chr15:75280522-75280531
10	MAX	chr15:75280379-75280712	NB4	blood:	n/a	n/a
11	SIN3AK20	chr15:75280367-75280626	PANC-1	pancreas:	n/a	n/a
12	REST	chr15:75280407-75280624	U87	brain:	n/a	chr15:75280522-75280531
13	YY1	chr15:75280391-75280652	K562	blood:	n/a	n/a
14	RAD21	chr15:75280288-75280819	HepG2	liver:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
15	CTCF	chr15:75280399-75280741	H1-hESC	embryonic stem cell:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
16	REST	chr15:75279964-75280869	A549	lung:	n/a	chr15:75280522-75280531
17	REST	chr15:75280260-75280826	ECC-1	luminal epithelium:	n/a	chr15:75280522-75280531
18	RAD21	chr15:75280396-75280655	GM12878	blood:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
19	CTCF	chr15:75280233-75280709	K562	blood:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
20	REST	chr15:75280309-75280722	HepG2	liver:	n/a	chr15:75280522-75280531
21	RAD21	chr15:75280328-75280851	ECC-1	luminal epithelium:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
22	CTCF	chr15:75280362-75280784	MCF-7	breast:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
23	MAX	chr15:75280408-75280639	K562	blood:	n/a	n/a
24	CTCF	chr15:75280407-75280705	MCF-7	breast:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
25	REST	chr15:75280278-75280659	U87	brain:	n/a	chr15:75280522-75280531
26	YY1	chr15:75280368-75280667	K562	blood:	n/a	n/a
27	CTCF	chr15:75280374-75280860	HCT-116	colon:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
28	EGR1	chr15:75280403-75280633	K562	blood:	n/a	n/a
29	REST	chr15:75280321-75280857	HCT-116	colon:	n/a	chr15:75280522-75280531
30	MAX	chr15:75280410-75280610	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOXA1	chr15:75280384-75280628	T-47D	breast:	n/a	n/a
32	RAD21	chr15:75280391-75280745	K562	blood:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
33	REST	chr15:75280251-75280773	MCF-7	breast:	n/a	chr15:75280522-75280531
34	REST	chr15:75280165-75280794	PFSK-1	brain:	n/a	chr15:75280522-75280531
35	REST	chr15:75280317-75280698	HCT-116	colon:	n/a	chr15:75280522-75280531
36	REST	chr15:75280169-75280739	HepG2	liver:	n/a	chr15:75280522-75280531
37	RAD21	chr15:75280359-75280706	SK-N-SH_RA	brain:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
38	CTCF	chr15:75280279-75280813	A549	lung:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
39	TCF3	chr15:75280420-75280605	GM12878	blood:	n/a	chr15:75280569-75280584
40	MAZ	chr15:75280366-75280704	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr15:75280416-75280687	MCF-7	breast:	n/a	chr15:75280567-75280580 chr15:75280565-75280583
42	MAZ	chr15:75280324-75280729	K562	blood:	n/a	n/a
43	SIN3AK20	chr15:75280396-75280622	PFSK-1	brain:	n/a	n/a
44	EGR1	chr15:75280425-75280631	K562	blood:	n/a	n/a
45	TCF12	chr15:75280398-75280644	GM12878	blood:	n/a	chr15:75280483-75280493 chr15:75280573-75280580
46	SMC3	chr15:75280419-75280754	HepG2	liver:	n/a	chr15:75280567-75280581
47	MAZ	chr15:75280297-75280849	IMR90	lung:	n/a	n/a
48	REST	chr15:75280334-75280630	GM12878	blood:	n/a	chr15:75280522-75280531
49	RAD21	chr15:75280330-75280896	MCF-7	breast:	n/a	chr15:75280567-75280577 chr15:75280569-75280578 chr15:75280403-75280415 chr15:75280566-75280579
50	ETS1	chr15:75280377-75280625	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75063135..75063986-chr15:75280277..75280997,2	MCF-7	breast:
2	chr15:75193631..75194372-chr15:75279911..75280528,2	MCF-7	breast:
3	chr15:75242403..75243361-chr15:75280099..75281035,2	MCF-7	breast:
4	chr15:75063133..75064034-chr15:75280031..75281063,7	MCF-7	breast:
5	chr15:75248236..75249066-chr15:75280065..75280985,3	MCF-7	breast:
6	chr15:75279778..75281928-chr15:75287388..75289491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199580	TF binding region
ENSG00000178718	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11072519	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12591175	0.82[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs12591994	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593476	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593542	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594117	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13056	0.89[LWK][hapmap]
rs2120019	0.84[LWK][hapmap]
rs2289582	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs2304903	0.89[LWK][hapmap]
rs2304904	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28394281	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3812943	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3812946	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816261	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs3910748	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55877218	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56828495	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56970592	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58068887	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58294763	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58403754	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58645417	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59094290	0.94[ASN][1000 genomes]
rs61166993	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495135	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495136	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495137	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495138	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495140	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495142	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166105	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs7167415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7168638	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172065	1.00[CEU][hapmap]
rs7172715	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172989	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173218	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7174129	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7179097	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182286	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7342591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7342601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73436579	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73436586	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73438537	0.85[ASN][1000 genomes]
rs73438554	0.86[AMR][1000 genomes]
rs74023908	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74025863	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028632	0.89[LWK][hapmap]
rs8031545	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034149	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036573	0.94[ASN][1000 genomes]
rs8040961	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672926	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672995	0.92[ASN][1000 genomes]
rs9672996	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9673012	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9788648	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1612	chr15:75247725-75281284	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7163390	SCAMP5	cis	Artery Tibial	GTEx
rs7163390	SCAMP5	cis	Thyroid	GTEx
rs7163390	PPCDC	cis	Adipose Subcutaneous	GTEx
rs7163390	SCAMP5	cis	multi-tissue	Pritchard
rs7163390	SCAMP5	cis	lymphoblastoid	seeQTL
rs7163390	SCAMP5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75279000-75280800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:75280400-75280600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr15:75280400-75280600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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