Variant report

Variant	rs4729575
Chromosome Location	chr7:99686873-99686874
allele	A/C/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	TCF12	chr7:99686153-99686894	ECC-1	luminal epithelium:	n/a	n/a
2	TAF1	chr7:99686262-99687197	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr7:99686801-99687047	SK-N-SH	brain:	n/a	n/a
4	HA-E2F1	chr7:99686178-99687184	MCF-7	breast:	n/a	chr7:99686580-99686589
5	RCOR1	chr7:99686288-99686933	K562	blood:	n/a	n/a
6	E2F4	chr7:99686080-99686965	K562	blood:	n/a	chr7:99686602-99686613 chr7:99686601-99686616 chr7:99686580-99686589
7	JUN	chr7:99685371-99687874	K562	blood:	n/a	chr7:99686473-99686482
8	ELF1	chr7:99686205-99687156	GM12878	blood:	n/a	chr7:99686825-99686837
9	MYC	chr7:99686804-99686978	MCF10A-Er-Src	breast:	n/a	n/a
10	REST	chr7:99686339-99686984	SK-N-SH	brain:	n/a	chr7:99686831-99686844
11	STAT1	chr7:99686329-99686995	GM12878	blood:	n/a	chr7:99686882-99686894
12	POLR2A	chr7:99686107-99687090	MCF-7	breast:	n/a	n/a
13	TEAD4	chr7:99686013-99687740	K562	blood:	n/a	n/a
14	POLR2A	chr7:99686127-99686906	GM12891	blood:	n/a	n/a
15	POLR2A	chr7:99686157-99687055	ECC-1	luminal epithelium:	n/a	n/a
16	TAF1	chr7:99686249-99687041	H1-neurons	neurons:	n/a	n/a
17	MAX	chr7:99685977-99687250	MCF-7	breast:	n/a	n/a
18	POLR2A	chr7:99686155-99686911	HUVEC	blood vessel:	n/a	n/a
19	YY1	chr7:99686273-99687114	GM12878	blood:	n/a	chr7:99686830-99686844 chr7:99686609-99686621 chr7:99686580-99686589
20	GTF2B	chr7:99686435-99687074	K562	blood:	n/a	n/a
21	SIN3AK20	chr7:99686255-99686889	PANC-1	pancreas:	n/a	n/a
22	JUND	chr7:99686069-99687036	MCF-7	breast:	n/a	chr7:99686473-99686482
23	POLR2A	chr7:99686221-99687111	Hela-S3	cervix:	n/a	n/a
24	TBP	chr7:99686338-99687046	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr7:99685821-99687101	GM12878	blood:	n/a	n/a
26	MAX	chr7:99686046-99687162	HepG2	liver:	n/a	n/a
27	MAX	chr7:99686108-99686992	HCT-116	colon:	n/a	n/a
28	YY1	chr7:99686097-99687483	SK-N-SH	brain:	n/a	chr7:99686830-99686844 chr7:99686609-99686621 chr7:99686580-99686589
29	POLR2A	chr7:99686112-99686993	GM12892	blood:	n/a	n/a
30	POLR2A	chr7:99686033-99687029	MCF-7	breast:	n/a	n/a
31	POLR2A	chr7:99686125-99686987	U87	brain:	n/a	n/a
32	MAX	chr7:99686206-99687145	H1-hESC	embryonic stem cell:	n/a	n/a
33	UBTF	chr7:99686116-99687213	K562	blood:	n/a	n/a
34	POLR2A	chr7:99685886-99687425	H1-hESC	embryonic stem cell:	n/a	n/a
35	SIN3AK20	chr7:99686626-99687125	H1-hESC	embryonic stem cell:	n/a	n/a
36	MXI1	chr7:99686297-99687446	Hela-S3	cervix:	n/a	n/a
37	BHLHE40	chr7:99686259-99687044	K562	blood:	n/a	n/a
38	REST	chr7:99686127-99687081	A549	lung:	n/a	chr7:99686831-99686844
39	MYC	chr7:99686178-99687048	K562	blood:	n/a	n/a
40	ZNF263	chr7:99686121-99687065	HEK293-T-REx	kidney:	n/a	chr7:99686766-99686775
41	ZBTB7A	chr7:99686787-99687127	K562	blood:	n/a	n/a
42	POLR2A	chr7:99686142-99687157	Hela-S3	cervix:	n/a	n/a
43	REST	chr7:99686231-99686938	H1-neurons	neurons:	n/a	chr7:99686831-99686844
44	TAF1	chr7:99686139-99687080	K562	blood:	n/a	n/a
45	MYC	chr7:99686141-99687155	K562	blood:	n/a	n/a
46	POLR2A	chr7:99686038-99686923	MCF-7	breast:	n/a	n/a
47	POLR2A	chr7:99685997-99687081	GM12878	blood:	n/a	n/a
48	TAF1	chr7:99686137-99687085	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr7:99686170-99686971	PBDE	blood:	n/a	n/a
50	MXI1	chr7:99685373-99687750	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:58893745..58894448-chr7:99686275..99686881,2	NB4	blood:
2	chr7:99686336..99688049-chr7:99754812..99756882,2	MCF-7	breast:
3	chr15:75493782..75494704-chr7:99686361..99687060,2	HCT-116	colon:
4	chr2:88355114..88355968-chr7:99686382..99686934,2	NB4	blood:
5	chr7:99612325..99614517-chr7:99685585..99687271,2	MCF-7	breast:
6	chr17:26879445..26879957-chr7:99686305..99686947,2	NB4	blood:

Variant related genes	Relation type
COPS6	TF binding region
ENSG00000109103	Chromatin interaction
ENSG00000100578	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000172086	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000100575	Chromatin interaction
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1122598	0.80[ASN][1000 genomes]
rs11558475	0.82[JPT][hapmap];0.81[MKK][hapmap]
rs11558476	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs11762932	0.81[MKK][hapmap]
rs11770546	0.84[ASN][1000 genomes]
rs12267	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531809	0.87[ASN][1000 genomes]
rs12532238	0.82[JPT][hapmap];0.84[MKK][hapmap]
rs12673441	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13238380	0.87[ASN][1000 genomes]
rs2261360	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2897075	0.87[ASN][1000 genomes]
rs35228488	0.87[ASN][1000 genomes]
rs4727445	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs4729573	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6592	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs6962405	1.00[YRI][hapmap]
rs6963345	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs72615159	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73158411	0.86[ASN][1000 genomes]
rs7789890	0.81[MKK][hapmap]
rs7803317	0.82[JPT][hapmap];0.81[MKK][hapmap]
rs941288	0.83[MKK][hapmap]
rs941289	0.82[JPT][hapmap];0.84[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4729575	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs4729575	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs4729575	TRIM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99685800-99687400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:99685800-99687400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr7:99685800-99687400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:99685800-99687600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:99685800-99689800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:99686000-99687000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:99686000-99687000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:99686000-99687200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:99686000-99687200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:99686000-99687200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr7:99686000-99687200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:99686000-99687200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:99686000-99687200	Active TSS	HSMMtube	muscle
14	chr7:99686000-99687400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr7:99686000-99687400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr7:99686000-99687400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr7:99686000-99687400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr7:99686000-99687400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr7:99686000-99687400	Flanking Active TSS	Fetal Thymus	thymus
20	chr7:99686000-99687400	Active TSS	Psoas Muscle	Psoas
21	chr7:99686000-99687600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr7:99686000-99687600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr7:99686000-99687800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr7:99686200-99687000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:99686200-99687000	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr7:99686200-99687000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:99686200-99687000	Active TSS	Aorta	Aorta
28	chr7:99686200-99687000	Active TSS	Brain Angular Gyrus	brain
29	chr7:99686200-99687000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr7:99686200-99687000	Active TSS	Fetal Brain Male	brain
31	chr7:99686200-99687000	Active TSS	Gastric	stomach
32	chr7:99686200-99687000	Active TSS	Lung	lung
33	chr7:99686200-99687000	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr7:99686200-99687000	Active TSS	Spleen	Spleen
35	chr7:99686200-99687200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:99686200-99687200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr7:99686200-99687200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:99686200-99687200	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr7:99686200-99687200	Active TSS	Small Intestine	intestine
40	chr7:99686200-99687400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:99686200-99687400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:99686200-99687400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:99686200-99687400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:99686200-99687400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr7:99686200-99687400	Active TSS	Esophagus	oesophagus
46	chr7:99686200-99687400	Active TSS	Ovary	ovary
47	chr7:99686200-99687600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr7:99686200-99687600	Flanking Active TSS	NH-A	brain
49	chr7:99686400-99687000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:99686400-99687000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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