Variant report

Variant	rs7734561
Chromosome Location	chr5:1594096-1594097
allele	A/G
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	POLR2A	chr5:1593754-1594250	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:1593846-1595062	GM12878	blood:	n/a	n/a
3	ZBTB7A	chr5:1594072-1594249	HepG2	liver:	n/a	n/a
4	HEY1	chr5:1593831-1594757	K562	blood:	n/a	n/a
5	POLR2A	chr5:1593574-1595153	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:1594059-1595070	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr5:1593680-1595156	GM12892	blood:	n/a	n/a
8	HEY1	chr5:1593757-1595375	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:1594087-1595040	MCF-7	breast:	n/a	n/a
10	POLR2A	chr5:1593687-1595340	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:1593752-1594097	Hela-S3	cervix:	n/a	n/a
12	ZNF263	chr5:1593962-1595124	HEK293-T-REx	kidney:	n/a	chr5:1594163-1594172
13	POLR2A	chr5:1593627-1595019	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:1593811-1595004	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:1593733-1594929	GM12891	blood:	n/a	n/a
16	POLR2A	chr5:1594051-1594992	GM12878	blood:	n/a	n/a
17	NR2F2	chr5:1594014-1595192	MCF-7	breast:	n/a	n/a
18	POLR2A	chr5:1593725-1594142	GM12891	blood:	n/a	n/a
19	TAF1	chr5:1593820-1595043	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:1593785-1594169	GM12892	blood:	n/a	n/a
21	MTA3	chr5:1593943-1594999	GM12878	blood:	n/a	n/a
22	HCFC1	chr5:1593989-1595151	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:1593842-1594146	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr5:1594080-1594230	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1521816..1527528-chr5:1592860..1598605,11	MCF-7	breast:
2	chr5:1523398..1525514-chr5:1593049..1596124,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271119	TF binding region
SDHAP3	TF binding region
ENSG00000248126	TF binding region
ENSG00000153395	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10043201	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10052477	0.89[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs10062417	0.85[ASN][1000 genomes]
rs10064943	0.83[ASN][1000 genomes]
rs1048186	0.85[ASN][1000 genomes]
rs11955318	0.94[ASN][1000 genomes]
rs11958585	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12153695	0.88[JPT][hapmap]
rs41408448	0.83[GIH][hapmap];0.89[JPT][hapmap]
rs6554915	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs6862954	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6897545	0.83[ASN][1000 genomes]
rs7710273	0.85[ASN][1000 genomes]
rs7734433	0.98[ASN][1000 genomes]
rs9312899	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312909	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9885250	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881664	chr5:1377172-1594879	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers 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	96 gene(s)	inside rSNPs	diseases
3	nsv880471	chr5:1466813-1598468	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
5	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
6	nsv881644	chr5:1478021-1597272	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
8	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
9	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv881574	chr5:1537141-1598468	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv881282	chr5:1549771-1597272	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs7734561	RP11-43F13.1	cis	Adipose Subcutaneous	GTEx
rs7734561	RP11-43F13.1	cis	lung	GTEx
rs7734561	PDCD6	cis	uninvolved skin	skin_eQTL
rs7734561	CTD-2012J19.1	cis	Muscle Skeletal	GTEx
rs7734561	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs7734561	RP11-43F13.1	cis	Artery Aorta	GTEx
rs7734561	CTD-2012J19.1	cis	Adipose Subcutaneous	GTEx
rs7734561	RP11-43F13.1	cis	Esophagus Muscularis	GTEx
rs7734561	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs7734561	PDCD6///LOC650280///LOC653378	cis	uninvolved skin	skin_eQTL
rs7734561	RP11-43F13.1	cis	Whole Blood	GTEx
rs7734561	RP11-43F13.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7734561	RP11-43F13.1	cis	Muscle Skeletal	GTEx
rs7734561	CTD-2012J19.1	cis	Thyroid	GTEx
rs7734561	CTD-2012J19.1	cis	Artery Tibial	GTEx
rs7734561	PDCD6	cis	lesional skin	skin_eQTL
rs7734561	Contig29802_RC	cis	multi-tissue	Pritchard
rs7734561	CTD-2012J19.1	cis	Esophagus Muscularis	GTEx
rs7734561	RP11-43F13.1	cis	Artery Tibial	GTEx
rs7734561	PDCD6///LOC650280///LOC653378	cis	lesional skin	skin_eQTL
rs7734561	CTD-2012J19.1	cis	lung	GTEx
rs7734561	CTD-2012J19.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7734561	CTD-2012J19.1	cis	Stomach	GTEx
rs7734561	RP11-43F13.1	cis	Heart Left Ventricle	GTEx
rs7734561	CTD-2012J19.1	cis	Nerve Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1565800-1594200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:1566200-1594200	Weak transcription	Brain Substantia Nigra	brain
3	chr5:1568800-1594200	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:1568800-1594200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:1569000-1594200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:1569000-1594200	Weak transcription	Psoas Muscle	Psoas
7	chr5:1569400-1594200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:1569600-1594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:1571200-1594400	Weak transcription	Stomach Mucosa	stomach
10	chr5:1573200-1594200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:1582400-1595000	Weak transcription	Fetal Heart	heart
12	chr5:1588200-1594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:1588800-1594200	Weak transcription	Aorta	Aorta
14	chr5:1588800-1594200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:1592800-1594200	Weak transcription	Liver	Liver
16	chr5:1593200-1595000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr5:1593200-1595400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr5:1593400-1595000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:1593400-1595200	Active TSS	GM12878-XiMat	blood
20	chr5:1593400-1595400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:1593400-1595400	Active TSS	Brain Germinal Matrix	brain
22	chr5:1593600-1595200	Active TSS	HepG2	liver
23	chr5:1593600-1595400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr5:1593800-1594400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:1593800-1594600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:1593800-1595000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr5:1593800-1595000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr5:1593800-1595200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr5:1593800-1595200	Active TSS	Hela-S3	cervix
30	chr5:1593800-1595400	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr5:1593800-1595400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:1593800-1595400	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr5:1593800-1595400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:1593800-1595400	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:1593800-1595400	Active TSS	Fetal Brain Female	brain
36	chr5:1594000-1594200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
37	chr5:1594000-1594200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
38	chr5:1594000-1594200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr5:1594000-1594200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr5:1594000-1594200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:1594000-1594200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:1594000-1594200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:1594000-1594200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:1594000-1594200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:1594000-1594200	Active TSS	Adipose Nuclei	Adipose
46	chr5:1594000-1594200	Flanking Active TSS	Colonic Mucosa	Colon
47	chr5:1594000-1594200	Flanking Active TSS	Fetal Brain Male	brain
48	chr5:1594000-1594200	Flanking Active TSS	Fetal Kidney	kidney
49	chr5:1594000-1594200	Active TSS	Placenta	Placenta
50	chr5:1594000-1594200	Active TSS	Lung	lung

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