Variant report

Variant	rs7649598
Chromosome Location	chr3:100053083-100053084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr3:100053039-100053623	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:100052685-100054939	HepG2	liver:	n/a	n/a
3	PML	chr3:100052936-100053916	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:100053059-100054674	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr3:100052857-100054783	SK-N-SH	brain:	n/a	n/a
6	CREB1	chr3:100052886-100054150	HepG2	liver:	n/a	n/a
7	MXI1	chr3:100053051-100054207	IMR90	lung:	n/a	n/a
8	TBP	chr3:100053032-100053819	HepG2	liver:	n/a	n/a
9	TAF7	chr3:100053080-100053665	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:100052816-100054186	HepG2	liver:	n/a	n/a
11	TAF1	chr3:100053014-100053957	H1-hESC	embryonic stem cell:	n/a	n/a
12	MTA3	chr3:100052935-100053658	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:100053030-100054041	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr3:100053065-100053722	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:100053083-100054826	GM12892	blood:	n/a	n/a
16	SIN3A	chr3:100052952-100054519	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOXA1	chr3:100053017-100053557	HepG2	liver:	n/a	n/a
18	BHLHE40	chr3:100053066-100053929	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:100053052-100055002	HepG2	liver:	n/a	n/a
20	MAX	chr3:100052837-100054148	HepG2	liver:	n/a	n/a
21	CTBP2	chr3:100052969-100054130	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:100053073-100054731	Raji	blood:	n/a	n/a
23	TAF1	chr3:100053075-100054139	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr3:100052996-100054047	HepG2	liver:	n/a	n/a
25	MYBL2	chr3:100053014-100053763	HepG2	liver:	n/a	n/a
26	RCOR1	chr3:100053025-100053690	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:100053055-100053980	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:100053047-100053953	ProgFib	skin:	n/a	n/a
29	FOXA1	chr3:100052959-100053771	HepG2	liver:	n/a	n/a
30	USF2	chr3:100052984-100053465	HepG2	liver:	n/a	n/a
31	SMARCC1	chr3:100053026-100054431	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr3:100053049-100054066	HepG2	liver:	n/a	chr3:100053222-100053230 chr3:100053427-100053438
33	HA-E2F1	chr3:100052975-100054278	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:100052864-100054196	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYBL2	chr3:100053032-100053738	HepG2	liver:	n/a	n/a
36	MBD4	chr3:100053006-100053550	HepG2	liver:	n/a	n/a
37	TBP	chr3:100053042-100054031	H1-hESC	embryonic stem cell:	n/a	n/a
38	MXI1	chr3:100053070-100053674	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:100053070-100053120	HNPCEpiC	eye:	n/a
2	chr3:100053070-100053120	HUVEC	blood vessel:	n/a
3	chr3:100053070-100053120	HCF	heart:	n/a
4	chr3:100053070-100053120	AG04449	skin:	fetal
5	chr3:100053070-100053120	HCT-116	colon:	n/a
6	chr3:100053070-100053120	SKMC	muscle:	n/a
7	chr3:100053070-100053120	BJ	skin:	n/a
8	chr3:100053070-100053120	Hela-S3	cervix:	n/a
9	chr3:100053070-100053120	PFSK-1	brain:	n/a
10	chr3:100053070-100053120	GM19239	blood:	n/a
11	chr3:100053070-100053120	RPTEC	kidney:	n/a
12	chr3:100053070-100053120	MCF10A-Er-Src	breast:	n/a
13	chr3:100053070-100053120	Hepatocyte	liver:	n/a
14	chr3:100053070-100053120	K562	blood:	n/a
15	chr3:100053070-100053120	HRCEpiC	kidney:	n/a
16	chr3:100053070-100053120	GM12892	blood:	n/a
17	chr3:100053070-100053120	H1-hESC	embryonic stem cell:	embryo
18	chr3:100053070-100053120	HCPEpiC	choroid plexus:	n/a
19	chr3:100053070-100053120	U87	brain:	n/a
20	chr3:100053070-100053120	NHBE	bronchial:	n/a
21	chr3:100053070-100053120	CMK	blood:	n/a
22	chr3:100053070-100053120	ProgFib	skin:	n/a
23	chr3:100053070-100053120	LNCaP	prostate:	n/a
24	chr3:100053070-100053120	HAEpiC	amniotic membrane:	n/a
25	chr3:100053070-100053120	GM12878	blood:	n/a
26	chr3:100053070-100053120	SK-N-MC	brain:	n/a
27	chr3:100053070-100053120	NH-A	brain:	n/a
28	chr3:100053070-100053120	HEEpiC	esophagus:	n/a
29	chr3:100053070-100053120	HL-60	blood:	n/a
30	chr3:100053070-100053120	HepG2	liver:	n/a
31	chr3:100053070-100053120	GM12891	blood:	n/a
32	chr3:100053070-100053120	HPAEpiC	pulmonary alveolar:	n/a
33	chr3:100053070-100053120	SAEC	small airway:	n/a
34	chr3:100053070-100053120	AG09309	skin:	n/a
35	chr3:100053070-100053120	AG09319	gingival:	n/a
36	chr3:100053070-100053120	PrEC	prostate:	n/a
37	chr3:100053070-100053120	HMEC	breast:	n/a
38	chr3:100053070-100053120	T-47D	breast:	n/a
39	chr3:100053070-100053120	ovcar-3	ovarian:	n/a
40	chr3:100053070-100053120	HRE	kidney:	n/a
41	chr3:100053070-100053120	HEK293	kidney:	embryo
42	chr3:100053070-100053120	NB4	blood:	n/a
43	chr3:100053070-100053120	SK-N-SH	brain:	n/a
44	chr3:100053070-100053120	PANC-1	pancreas:	n/a
45	chr3:100053070-100053120	MCF-7	breast:	n/a
46	chr3:100053070-100053120	Jurkat	blood:	n/a
47	chr3:100053070-100053120	HIPEpiC	eye:	n/a
48	chr3:100053070-100053120	IMR90	lung:	fetal
49	chr3:100053070-100053120	ECC-1	luminal epithelium:	n/a
50	chr3:100053070-100053120	AoSMC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:

No data

Variant related genes	Relation type
NIT2	TF binding region
NIT2	CpG island
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1045206	0.80[CEU][hapmap]
rs11714045	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214375	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs13071905	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13073252	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs13082297	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1486308	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1561743	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2289502	0.91[ASN][1000 genomes]
rs2289505	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289506	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34645158	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35281373	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35945684	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772693	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4441690	0.81[ASN][1000 genomes]
rs4928123	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4928125	0.96[CEU][hapmap]
rs61436017	0.90[ASN][1000 genomes]
rs62274141	0.84[ASN][1000 genomes]
rs62274146	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62274147	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73150352	0.82[ASN][1000 genomes]
rs756103	0.81[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7649598	OR5H6	cis	cerebellum	SCAN
rs7649598	IMPG2	cis	cerebellum	SCAN
rs7649598	NIT2	cis	parietal	SCAN
rs7649598	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs7649598	C3orf26	cis	cerebellum	SCAN
rs7649598	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100053200	Weak transcription	Gastric	stomach
2	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:100049400-100053600	Weak transcription	Spleen	Spleen
4	chr3:100052600-100053400	Flanking Active TSS	Liver	Liver
5	chr3:100052800-100053200	Enhancers	Fetal Thymus	thymus
6	chr3:100052800-100053400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr3:100052800-100053400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr3:100052800-100053400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:100052800-100053400	Flanking Active TSS	Dnd41	blood
10	chr3:100052800-100054000	Active TSS	Stomach Smooth Muscle	stomach
11	chr3:100052800-100054200	Active TSS	Fetal Kidney	kidney
12	chr3:100052800-100054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:100052800-100054600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:100052800-100054800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:100052800-100054800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:100053000-100053200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr3:100053000-100053200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
18	chr3:100053000-100053200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:100053000-100053200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:100053000-100053200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr3:100053000-100053200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:100053000-100053200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:100053000-100053200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr3:100053000-100053200	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr3:100053000-100053200	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr3:100053000-100053200	Flanking Active TSS	Fetal Brain Female	brain
27	chr3:100053000-100053200	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr3:100053000-100053200	Enhancers	Lung	lung
29	chr3:100053000-100053200	Flanking Active TSS	Right Ventricle	heart
30	chr3:100053000-100053200	Enhancers	Small Intestine	intestine
31	chr3:100053000-100053200	Flanking Active TSS	Thymus	Thymus
32	chr3:100053000-100053200	Flanking Active TSS	HepG2	liver
33	chr3:100053000-100053200	Enhancers	K562	blood
34	chr3:100053000-100053400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:100053000-100053400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:100053000-100053400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:100053000-100053400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:100053000-100053400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr3:100053000-100053400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:100053000-100053400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:100053000-100053400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:100053000-100053400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr3:100053000-100053400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr3:100053000-100053400	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr3:100053000-100053400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr3:100053000-100053400	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr3:100053000-100053400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr3:100053000-100053400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:100053000-100053400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:100053000-100053400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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