Variant report

Variant	rs3736591
Chromosome Location	chr7:99751017-99751018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99750857-99753098	K562	blood:	n/a	n/a
2	POLR2A	chr7:99750884-99752952	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:99750857-99751080	HCT-116	colon:	n/a	n/a
4	POLR2A	chr7:99751000-99752584	K562	blood:	n/a	n/a
5	POLR2A	chr7:99750901-99752568	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:99750726-99751996	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF263	chr7:99750885-99752112	HEK293-T-REx	kidney:	n/a	n/a
8	POLR2A	chr7:99750790-99752112	HL-60	blood:	n/a	n/a
9	CCNT2	chr7:99750965-99751220	K562	blood:	n/a	n/a
10	POLR2A	chr7:99750175-99756739	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr7:99750655-99753889	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr7:99750866-99751695	U87	brain:	n/a	n/a
13	POLR2A	chr7:99750788-99752014	HepG2	liver:	n/a	n/a
14	POLR2A	chr7:99750934-99751131	HepG2	liver:	n/a	n/a
15	PBX3	chr7:99750753-99751904	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr7:99750893-99751216	A549	lung:	n/a	n/a
17	POLR2A	chr7:99750928-99751937	HepG2	liver:	n/a	n/a
18	POLR2A	chr7:99750581-99752055	K562	blood:	n/a	n/a
19	POLR2A	chr7:99749057-99752067	HepG2	liver:	n/a	n/a
20	POLR2A	chr7:99750885-99753393	K562	blood:	n/a	n/a
21	HMGN3	chr7:99750951-99751079	K562	blood:	n/a	n/a
22	POLR2A	chr7:99750911-99751099	A549	lung:	n/a	n/a
23	POLR2A	chr7:99750867-99751150	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr7:99750884-99751182	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:99750513-99752750	PFSK-1	brain:	n/a	n/a
26	HEY1	chr7:99750884-99751140	K562	blood:	n/a	n/a
27	POLR2A	chr7:99750843-99751701	U87	brain:	n/a	n/a
28	POLR2A	chr7:99750795-99752035	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr7:99750656-99753129	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr7:99749956-99756618	K562	blood:	n/a	n/a
31	POLR2A	chr7:99750874-99751180	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:99750754-99752008	GM12892	blood:	n/a	n/a
33	POLR2A	chr7:99750949-99751162	ProgFib	skin:	n/a	n/a
34	POLR2A	chr7:99750876-99751507	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr7:99749910-99757285	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr7:99750585-99756760	K562	blood:	n/a	n/a
37	POLR2A	chr7:99750942-99751657	K562	blood:	n/a	n/a
38	POLR2A	chr7:99750868-99751216	U87	brain:	n/a	n/a
39	POLR2A	chr7:99750952-99751138	A549	lung:	n/a	n/a
40	POLR2A	chr7:99750816-99751167	MCF-7	breast:	n/a	n/a
41	POLR2A	chr7:99750752-99753381	K562	blood:	n/a	n/a
42	POLR2A	chr7:99750877-99751140	HCT-116	colon:	n/a	n/a
43	POLR2A	chr7:99751017-99751152	GM12878	blood:	n/a	n/a
44	POLR2A	chr7:99749991-99753002	GM12891	blood:	n/a	n/a
45	POLR2A	chr7:99750905-99751243	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr7:99750807-99751144	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr7:99750828-99751394	GM12878	blood:	n/a	n/a
48	POLR2A	chr7:99750868-99751139	HepG2	liver:	n/a	n/a
49	POLR2A	chr7:99750041-99756801	K562	blood:	n/a	n/a
50	POLR2A	chr7:99750954-99751100	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99749770..99752333-chr7:99765768..99768227,2	MCF-7	breast:
2	chr7:99750795..99756202-chr7:99762627..99766634,7	K562	blood:
3	chr7:99696898..99700086-chr7:99750657..99754674,4	MCF-7	breast:
4	chr7:99750253..99753026-chr7:99768043..99770127,2	MCF-7	breast:

No data

Variant related genes	Relation type
LAMTOR4	TF binding region
ENSG00000213420	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000197093	Chromatin interaction
ENSG00000221838	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10231604	0.88[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs11764584	0.88[GIH][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs12878	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1918353	0.84[GIH][hapmap]
rs2272337	0.88[GIH][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs2272338	0.94[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs2405440	0.83[YRI][hapmap]
rs35042434	0.81[ASN][1000 genomes]
rs3736590	0.88[GIH][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs3779047	0.81[ASN][1000 genomes]
rs3800951	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs3807479	0.96[YRI][hapmap]
rs3823646	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs4134917	0.94[ASW][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs4729568	0.84[ASW][hapmap];0.96[YRI][hapmap]
rs4729577	0.94[ASW][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap]
rs6960432	0.93[YRI][hapmap]
rs7785392	0.88[GIH][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs9649220	0.84[ASW][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
9	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
10	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3736591	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs3736591	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs3736591	ZKSCAN1	cis	multi-tissue	Pritchard
rs3736591	ZSCAN21	cis	parietal	SCAN
rs3736591	AP4M1	cis	Artery Tibial	GTEx
rs3736591	AP4M1	cis	lymphoblastoid	seeQTL
rs3736591	AP4M1	cis	Whole Blood	GTEx
rs3736591	AP4M1	cis	Esophagus Muscularis	GTEx
rs3736591	MBLAC1	cis	cerebellum	SCAN
rs3736591	AP4M1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99747200-99751400	Weak transcription	Aorta	Aorta
2	chr7:99747400-99753000	Weak transcription	Ovary	ovary
3	chr7:99747400-99753000	Weak transcription	HSMM	muscle
4	chr7:99747400-99753400	Weak transcription	HSMMtube	muscle
5	chr7:99747400-99754600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:99747400-99754600	Weak transcription	Fetal Heart	heart
7	chr7:99747400-99754600	Weak transcription	Right Atrium	heart
8	chr7:99747400-99755200	Weak transcription	Psoas Muscle	Psoas
9	chr7:99747400-99755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:99747600-99753400	Weak transcription	NH-A	brain
11	chr7:99747800-99751200	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr7:99747800-99753400	Weak transcription	Fetal Kidney	kidney
13	chr7:99747800-99754600	Weak transcription	HUVEC	blood vessel
14	chr7:99748000-99751200	Weak transcription	Brain Substantia Nigra	brain
15	chr7:99748000-99751600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:99748000-99753400	Weak transcription	Brain Angular Gyrus	brain
17	chr7:99748000-99755200	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr7:99748200-99751200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:99748200-99751200	Weak transcription	Small Intestine	intestine
20	chr7:99748200-99753400	Weak transcription	NHDF-Ad	bronchial
21	chr7:99748200-99754200	Weak transcription	Fetal Brain Male	brain
22	chr7:99748400-99751200	Weak transcription	NHEK	skin
23	chr7:99748400-99751400	Enhancers	Primary B cells from cord blood	blood
24	chr7:99749000-99754400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:99749000-99754400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:99749200-99751200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:99749200-99751200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr7:99749200-99752600	Strong transcription	Lung	lung
29	chr7:99749200-99753800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:99749200-99754400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr7:99749200-99754600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:99749200-99755000	Genic enhancers	Fetal Intestine Large	intestine
33	chr7:99749400-99751200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:99749400-99751600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:99749400-99751800	Genic enhancers	GM12878-XiMat	blood
36	chr7:99749400-99752200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr7:99749400-99752400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:99749400-99752400	Strong transcription	Brain Cingulate Gyrus	brain
39	chr7:99749400-99752600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:99749400-99752600	Enhancers	HepG2	liver
41	chr7:99749400-99754200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:99749400-99754200	Strong transcription	Fetal Muscle Leg	muscle
43	chr7:99749400-99754400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr7:99749400-99754400	Genic enhancers	Placenta	Placenta
45	chr7:99749400-99754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:99749400-99754600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:99749400-99754600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr7:99749400-99754600	Strong transcription	Fetal Stomach	stomach
49	chr7:99749400-99754800	Genic enhancers	Fetal Intestine Small	intestine
50	chr7:99749400-99754800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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