Variant report

Variant	rs2713933
Chromosome Location	chr15:56538562-56538563
allele	A/C
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	RFX5	chr15:56537974-56538619	Hela-S3	cervix:	n/a	chr15:56538106-56538122
2	GATA3	chr15:56538201-56538624	T-47D	breast:	n/a	n/a
3	RFX5	chr15:56538222-56538707	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD1	chr15:56538127-56538620	IMR90	lung:	n/a	n/a
5	MYBL2	chr15:56538087-56538700	HepG2	liver:	n/a	n/a
6	CTCF	chr15:56538237-56538572	Lung_OC	lung:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
7	CTCF	chr15:56537960-56538693	MCF-7	breast:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
8	ZNF143	chr15:56538072-56538604	Hela-S3	cervix:	n/a	n/a
9	RCOR1	chr15:56538048-56538620	Hela-S3	cervix:	n/a	n/a
10	ATF3	chr15:56537992-56538653	A549	lung:	n/a	n/a
11	RAD21	chr15:56538103-56538674	Hela-S3	cervix:	n/a	chr15:56538403-56538417 chr15:56538416-56538429 chr15:56538415-56538427 chr15:56538384-56538391 chr15:56538407-56538420 chr15:56538382-56538401 chr15:56538386-56538395 chr15:56538413-56538432
12	CEBPB	chr15:56538009-56538659	A549	lung:	n/a	n/a
13	SP1	chr15:56537915-56538729	A549	lung:	n/a	chr15:56538576-56538583
14	SP4	chr15:56538050-56538611	H1-hESC	embryonic stem cell:	n/a	n/a
15	RCOR1	chr15:56538230-56538613	HepG2	liver:	n/a	n/a
16	CTCF	chr15:56538222-56538585	A549	lung:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
17	CTCF	chr15:56538235-56538575	HUVEC	blood vessel:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
18	SIN3AK20	chr15:56538167-56538657	A549	lung:	n/a	n/a
19	IRF1	chr15:56538065-56538571	K562	blood:	n/a	chr15:56538198-56538207
20	BCLAF1	chr15:56538030-56538602	K562	blood:	n/a	chr15:56538404-56538417
21	TEAD4	chr15:56537963-56538647	K562	blood:	n/a	n/a
22	EP300	chr15:56538171-56538581	H1-hESC	embryonic stem cell:	n/a	chr15:56538368-56538384 chr15:56538403-56538419
23	KAP1	chr15:56538126-56538609	HEK293	kidney:	n/a	n/a
24	NFYA	chr15:56538026-56538902	Hela-S3	cervix:	n/a	n/a
25	MAX	chr15:56538068-56538603	GM12878	blood:	n/a	n/a
26	MYC	chr15:56538276-56538650	H1-hESC	embryonic stem cell:	n/a	n/a
27	CHD2	chr15:56537969-56538741	GM12878	blood:	n/a	n/a
28	MAX	chr15:56538017-56538658	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr15:56537988-56538576	NB4	blood:	n/a	n/a
30	TAL1	chr15:56538040-56538571	K562	blood:	n/a	n/a
31	SIN3AK20	chr15:56538061-56538611	SK-N-SH	brain:	n/a	n/a
32	TAF7	chr15:56538070-56538607	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF1	chr15:56538002-56538606	H1-hESC	embryonic stem cell:	n/a	n/a
34	ELF1	chr15:56538170-56538698	GM12878	blood:	n/a	n/a
35	TCF7L2	chr15:56537923-56538631	PANC-1	pancreas:	n/a	n/a
36	POU2F2	chr15:56537952-56538619	GM12878	blood:	n/a	n/a
37	REST	chr15:56537855-56538695	A549	lung:	n/a	n/a
38	CTCF	chr15:56538251-56538583	MCF-7	breast:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
39	CEBPB	chr15:56537864-56538682	A549	lung:	n/a	chr15:56538666-56538679
40	TAF1	chr15:56538063-56538584	ECC-1	luminal epithelium:	n/a	n/a
41	RXRA	chr15:56538203-56538591	H1-hESC	embryonic stem cell:	n/a	chr15:56538413-56538433
42	MYC	chr15:56535595-56538658	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847
43	USF2	chr15:56538170-56538670	H1-hESC	embryonic stem cell:	n/a	n/a
44	RCOR1	chr15:56534834-56538657	K562	blood:	n/a	n/a
45	CTCF	chr15:56538202-56538583	GM12892	blood:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
46	CTCF	chr15:56538018-56538845	MCF-7	breast:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
47	MAZ	chr15:56538027-56538706	K562	blood:	n/a	n/a
48	ZKSCAN1	chr15:56538164-56538596	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr15:56538251-56538568	LNCaP	prostate:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
50	TAF1	chr15:56537999-56538566	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:56369125..56370857-chr15:56537851..56540743,2	K562	blood:
2	chr15:56538148..56538680-chr20:45843538..45844107,2	MCF-7	breast:
3	chr12:75413695..75414606-chr15:56538291..56538861,2	MCF-7	breast:
4	chr15:56285427..56286973-chr15:56537527..56538833,7	MCF-7	breast:
5	chr15:56536983..56539715-chr15:56539921..56543667,5	K562	blood:
6	chr15:56537725..56539025-chr15:56720287..56722326,16	MCF-7	breast:
7	chr15:56478637..56480315-chr15:56536798..56538580,2	K562	blood:
8	chr15:56537986..56539019-chr15:56720847..56721772,4	K562	blood:
9	chr15:56344670..56345334-chr15:56537961..56538799,2	MCF-7	breast:
10	chr15:56189903..56190536-chr15:56538041..56538735,3	MCF-7	breast:
11	chr15:56453020..56453777-chr15:56537985..56538862,2	MCF-7	breast:
12	chr15:56538080..56538849-chr15:56720711..56721356,4	MCF-7	breast:
13	chr15:56282050..56287467-chr15:56534024..56538662,8	MCF-7	breast:
14	chr15:56483194..56486063-chr15:56535825..56539303,3	MCF-7	breast:
15	chr15:56536734..56539507-chr15:56718886..56721172,2	MCF-7	breast:
16	chr15:56538110..56538885-chr8:43094202..43095000,2	MCF-7	breast:
17	chr15:56309948..56310461-chr15:56538175..56538871,2	MCF-7	breast:
18	chr15:56537987..56538847-chr15:56756234..56756979,2	MCF-7	breast:
19	chr15:56345036..56345575-chr15:56538156..56538672,2	MCF-7	breast:
20	chr13:39989718..39990375-chr15:56538148..56538851,2	MCF-7	breast:
21	chr11:2545295..2546795-chr15:56536741..56538582,2	K562	blood:
22	chr15:55940342..55940845-chr15:56538253..56538849,2	MCF-7	breast:

Variant related genes	Relation type
RFX7	TF binding region
ENSG00000069869	Chromatin interaction
ENSG00000261072	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11629483	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630363	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs11631191	0.87[EUR][1000 genomes]
rs11855094	0.91[CHB][hapmap]
rs12900678	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs12905782	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12905899	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911094	0.92[CEU][hapmap]
rs12911427	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs12914640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1372753	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1549452	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs16976890	0.91[CHB][hapmap]
rs17819438	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap]
rs1829542	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2119937	0.92[CEU][hapmap]
rs2249090	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2303441	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2414464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2460647	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2460648	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2460650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2465973	0.83[AMR][1000 genomes]
rs2554287	0.91[CHB][hapmap]
rs2682044	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682046	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2682049	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682053	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682054	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682059	0.96[CEU][hapmap]
rs2713923	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713926	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2713931	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2713935	0.82[CEU][hapmap]
rs2713936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713938	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713941	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718915	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2718921	0.91[CHB][hapmap]
rs2718934	1.00[CEU][hapmap]
rs2718941	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2725854	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2725856	0.82[CHB][hapmap]
rs2725870	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2947021	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs34044869	0.80[AMR][1000 genomes]
rs34144128	0.80[AMR][1000 genomes]
rs35749329	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35972806	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3784552	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs3817406	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4310791	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774232	1.00[CEU][hapmap]
rs59432349	0.87[EUR][1000 genomes]
rs62044110	0.80[EUR][1000 genomes]
rs62044111	0.80[EUR][1000 genomes]
rs6493856	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6493858	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7168319	0.80[AMR][1000 genomes]
rs7170307	0.89[CEU][hapmap];0.93[JPT][hapmap]
rs7174823	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176107	0.80[CEU][hapmap]
rs7181235	0.91[CHB][hapmap]
rs7496025	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs795791	0.86[CHB][hapmap]
rs795800	0.91[CHB][hapmap]
rs8024031	0.92[CEU][hapmap]
rs8028353	0.80[AMR][1000 genomes]
rs8029114	0.80[AMR][1000 genomes]
rs9672886	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9672928	0.81[AMR][1000 genomes];0.82[EUR][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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2713933	RFX7	cis	Adipose Subcutaneous	GTEx
rs2713933	FLJ12994	cis	multi-tissue	Pritchard
rs2713933	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56536400-56538600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr15:56536400-56538600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:56536600-56538600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:56536800-56538600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr15:56536800-56538600	Enhancers	Stomach Mucosa	stomach
6	chr15:56536800-56538800	Flanking Active TSS	Dnd41	blood
7	chr15:56537000-56538600	Enhancers	Esophagus	oesophagus
8	chr15:56537000-56538600	Enhancers	Fetal Muscle Leg	muscle
9	chr15:56537000-56538600	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr15:56537000-56538800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:56537200-56538600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:56537200-56538800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:56537200-56538800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:56537600-56538600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:56537600-56539600	Weak transcription	Gastric	stomach
16	chr15:56537800-56540400	Weak transcription	Small Intestine	intestine
17	chr15:56538000-56538600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:56538000-56538600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:56538200-56538600	Active TSS	Primary T cells from cord blood	blood
20	chr15:56538200-56538600	Active TSS	Brain Cingulate Gyrus	brain
21	chr15:56538200-56538800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:56538200-56538800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr15:56538200-56538800	Active TSS	K562	blood
24	chr15:56538200-56539000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:56538200-56539600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:56538200-56546600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:56538400-56538600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:56538400-56538600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr15:56538400-56538600	Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr15:56538400-56538600	Enhancers	Primary T cells fromperipheralblood	blood
31	chr15:56538400-56538600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:56538400-56538600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr15:56538400-56538600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:56538400-56538600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:56538400-56538600	Enhancers	Brain Anterior Caudate	brain
36	chr15:56538400-56538600	Enhancers	Duodenum Mucosa	Duodenum
37	chr15:56538400-56538600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:56538400-56538600	Enhancers	Fetal Intestine Small	intestine
39	chr15:56538400-56538600	Enhancers	Placenta	Placenta
40	chr15:56538400-56538600	Enhancers	Fetal Thymus	thymus
41	chr15:56538400-56538600	Enhancers	Pancreas	Pancrea
42	chr15:56538400-56538600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr15:56538400-56538600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:56538400-56538600	Enhancers	HMEC	breast
45	chr15:56538400-56538600	Enhancers	NHEK	skin
46	chr15:56538400-56538800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr15:56538400-56538800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr15:56538400-56538800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:56538400-56538800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr15:56538400-56538800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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