Variant report

Variant	rs4147146
Chromosome Location	chr1:165567334-165567335
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	chr1:165567267-165567753	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr1:165567134-165567870	H1-hESC	embryonic stem cell:	n/a	chr1:165567154-165567162 chr1:165567152-165567163 chr1:165567153-165567163
3	ZNF143	chr1:165567300-165567630	Hela-S3	cervix:	n/a	n/a
4	MAX	chr1:165567102-165568043	A549	lung:	n/a	n/a
5	CHD2	chr1:165567294-165567651	H1-hESC	embryonic stem cell:	n/a	n/a
6	EGR1	chr1:165567196-165567839	MCF-7	breast:	n/a	chr1:165567590-165567600
7	ZNF384	chr1:165567289-165567798	K562	blood:	n/a	n/a
8	POLR2A	chr1:165567267-165568058	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:165567258-165567769	K562	blood:	n/a	n/a
10	POLR2A	chr1:165567264-165567755	Hela-S3	cervix:	n/a	n/a
11	SPI1	chr1:165567207-165567772	GM12891	blood:	n/a	n/a
12	SP2	chr1:165567310-165567752	HepG2	liver:	n/a	chr1:165567510-165567525
13	POLR2A	chr1:165567273-165567696	HUVEC	blood vessel:	n/a	n/a
14	TBL1XR1	chr1:165567303-165567546	K562	blood:	n/a	n/a
15	SREBP1	chr1:165567267-165567829	HepG2	liver:	n/a	chr1:165567421-165567435 chr1:165567422-165567436
16	E2F6	chr1:165567237-165567913	K562	blood:	n/a	n/a
17	CHD2	chr1:165567225-165567864	K562	blood:	n/a	n/a
18	POLR2A	chr1:165567261-165567758	Hela-S3	cervix:	n/a	n/a
19	CBX3	chr1:165567101-165568025	K562	blood:	n/a	n/a
20	TAF1	chr1:165567238-165567774	SK-N-SH	brain:	n/a	n/a
21	EGR1	chr1:165567195-165567715	H1-hESC	embryonic stem cell:	n/a	chr1:165567590-165567600
22	THAP1	chr1:165567244-165567682	K562	blood:	n/a	n/a
23	POLR2A	chr1:165567299-165567661	A549	lung:	n/a	n/a
24	MYC	chr1:165567037-165567707	MCF10A-Er-Src	breast:	n/a	n/a
25	EGR1	chr1:165567190-165567764	ECC-1	luminal epithelium:	n/a	chr1:165567590-165567600
26	SIN3A	chr1:165567166-165568046	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOS	chr1:165567290-165567812	K562	blood:	n/a	n/a
28	RFX5	chr1:165566947-165567925	Hela-S3	cervix:	n/a	chr1:165567421-165567436 chr1:165567420-165567437 chr1:165567429-165567437 chr1:165567421-165567436 chr1:165567385-165567399 chr1:165567421-165567436
29	TBP	chr1:165567255-165567913	K562	blood:	n/a	n/a
30	MYC	chr1:165567215-165567602	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr1:165567208-165567907	IMR90	lung:	n/a	n/a
32	EGR1	chr1:165567128-165567807	MCF-7	breast:	n/a	chr1:165567590-165567600
33	TBL1XR1	chr1:165566991-165567785	K562	blood:	n/a	n/a
34	IRF1	chr1:165567268-165567896	K562	blood:	n/a	chr1:165567590-165567604
35	HCFC1	chr1:165567273-165568301	K562	blood:	n/a	n/a
36	POLR2A	chr1:165567159-165568212	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr1:165567228-165567850	NB4	blood:	n/a	n/a
38	RCOR1	chr1:165567128-165568031	GM12878	blood:	n/a	n/a
39	E2F6	chr1:165567215-165567974	K562	blood:	n/a	n/a
40	ELF1	chr1:165567237-165567844	MCF-7	breast:	n/a	n/a
41	POLR2A	chr1:165567242-165567812	HCT-116	colon:	n/a	n/a
42	NRF1	chr1:165567299-165567667	K562	blood:	n/a	n/a
43	SP1	chr1:165567127-165567902	A549	lung:	n/a	chr1:165567590-165567602 chr1:165567590-165567602 chr1:165567592-165567601 chr1:165567587-165567601 chr1:165567590-165567601 chr1:165567591-165567601 chr1:165567591-165567600
44	CHD1	chr1:165567260-165567931	GM12878	blood:	n/a	n/a
45	CHD2	chr1:165567147-165567838	Hela-S3	cervix:	n/a	n/a
46	SIN3AK20	chr1:165567209-165567765	K562	blood:	n/a	n/a
47	EP300	chr1:165567220-165567976	GM12878	blood:	n/a	n/a
48	TBP	chr1:165567265-165567716	H1-hESC	embryonic stem cell:	n/a	n/a
49	EGR1	chr1:165567151-165567742	ECC-1	luminal epithelium:	n/a	chr1:165567590-165567600
50	RFX5	chr1:165567154-165567900	K562	blood:	n/a	chr1:165567421-165567436 chr1:165567420-165567437 chr1:165567429-165567437 chr1:165567421-165567436 chr1:165567385-165567399 chr1:165567421-165567436

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:165567312-165567362	GM06990	blood:	n/a
2	chr1:165567312-165567362	PANC-1	pancreas:	n/a
3	chr1:165567312-165567362	ProgFib	skin:	n/a
4	chr1:165567312-165567362	ECC-1	luminal epithelium:	n/a
5	chr1:165567312-165567362	HNPCEpiC	eye:	n/a
6	chr1:165567312-165567362	Hela-S3	cervix:	n/a
7	chr1:165567312-165567362	RPTEC	kidney:	n/a
8	chr1:165567312-165567362	AG04449	skin:	fetal
9	chr1:165567312-165567362	Hepatocyte	liver:	n/a
10	chr1:165567312-165567362	HUVEC	blood vessel:	n/a
11	chr1:165567312-165567362	H1-hESC	embryonic stem cell:	embryo
12	chr1:165567312-165567362	MCF10A-Er-Src	breast:	n/a
13	chr1:165567312-165567362	GM12878	blood:	n/a
14	chr1:165567312-165567362	NB4	blood:	n/a
15	chr1:165567312-165567362	PFSK-1	brain:	n/a
16	chr1:165567312-165567362	HRCEpiC	kidney:	n/a
17	chr1:165567312-165567362	HMEC	breast:	n/a
18	chr1:165567312-165567362	AG10803	skin:	n/a
19	chr1:165567312-165567362	NHBE	bronchial:	n/a
20	chr1:165567312-165567362	GM19239	blood:	n/a
21	chr1:165567312-165567362	AoSMC	blood vessel:	n/a
22	chr1:165567312-165567362	ovcar-3	ovarian:	n/a
23	chr1:165567312-165567362	NHDF-neo	bronchial:	n/a
24	chr1:165567312-165567362	HCM	heart:	n/a
25	chr1:165567312-165567362	K562	blood:	n/a
26	chr1:165567312-165567362	HPAEpiC	pulmonary alveolar:	n/a
27	chr1:165567312-165567362	HL-60	blood:	n/a
28	chr1:165567312-165567362	HepG2	liver:	n/a
29	chr1:165567312-165567362	A549	lung:	n/a
30	chr1:165567312-165567362	HIPEpiC	eye:	n/a
31	chr1:165567312-165567362	BE2_C	brain:	n/a
32	chr1:165567312-165567362	Jurkat	blood:	n/a
33	chr1:165567312-165567362	HRE	kidney:	n/a
34	chr1:165567312-165567362	GM12892	blood:	n/a
35	chr1:165567312-165567362	GM12891	blood:	n/a
36	chr1:165567312-165567362	LNCaP	prostate:	n/a
37	chr1:165567312-165567362	AG09309	skin:	n/a
38	chr1:165567312-165567362	SK-N-SH	brain:	n/a
39	chr1:165567312-165567362	U87	brain:	n/a
40	chr1:165567312-165567362	Caco-2	colon:	n/a
41	chr1:165567312-165567362	HCF	heart:	n/a
42	chr1:165567312-165567362	HCPEpiC	choroid plexus:	n/a
43	chr1:165567312-165567362	IMR90	lung:	fetal
44	chr1:165567312-165567362	T-47D	breast:	n/a
45	chr1:165567312-165567362	BJ	skin:	n/a
46	chr1:165567312-165567362	MCF-7	breast:	n/a
47	chr1:165567312-165567362	HEEpiC	esophagus:	n/a
48	chr1:165567312-165567362	SK-N-SH_RA	brain:	n/a
49	chr1:165567312-165567362	AG09319	gingival:	n/a
50	chr1:165567312-165567362	SK-N-MC	brain:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165564921..165568209-chr1:165795710..165798284,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGST3-1	chr1:165567006-165569013	NONHSAT007321

Variant related genes	Relation type
ENSG00000236206	TF binding region
ENSG00000236206	CpG island
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011469	0.91[CHB][hapmap]
rs1025159	0.82[CHB][hapmap]
rs12119602	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125420	0.88[EUR][1000 genomes]
rs12126717	0.91[CHB][hapmap]
rs12128974	0.91[EUR][1000 genomes]
rs12130157	0.88[EUR][1000 genomes]
rs12131992	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137629	0.91[CHB][hapmap]
rs12142477	0.85[EUR][1000 genomes]
rs12143824	0.91[CHB][hapmap]
rs1326374	0.91[CHB][hapmap]
rs1409413	0.80[AMR][1000 genomes]
rs16846623	0.91[CHB][hapmap]
rs16847331	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847398	0.80[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847570	0.92[CHB][hapmap]
rs1913836	0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs2152818	0.91[CHB][hapmap]
rs2252342	0.82[AMR][1000 genomes]
rs285422	0.91[CHB][hapmap]
rs285438	0.91[CHB][hapmap]
rs6669449	0.91[CHB][hapmap]
rs7521982	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs7539622	0.91[CHB][hapmap]
rs7554080	0.92[CHB][hapmap];0.91[EUR][1000 genomes]
rs927844	0.91[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429902	chr1:165531342-165574342	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165566600-165567400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:165566600-165567800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:165566600-165568000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr1:165566600-165568000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:165566800-165567400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
6	chr1:165566800-165567800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:165566800-165568000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:165566800-165568000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr1:165566800-165568000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr1:165566800-165568000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:165566800-165568000	Active TSS	Colonic Mucosa	Colon
12	chr1:165566800-165568000	Active TSS	Fetal Brain Male	brain
13	chr1:165566800-165568200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:165566800-165568200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr1:165566800-165568200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:165566800-165568200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:165566800-165568200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:165566800-165568200	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr1:165566800-165568200	Flanking Active TSS	Dnd41	blood
20	chr1:165566800-165568200	Flanking Active TSS	K562	blood
21	chr1:165566800-165568600	Active TSS	Brain Germinal Matrix	brain
22	chr1:165567000-165567400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr1:165567000-165567400	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr1:165567000-165567400	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr1:165567000-165567400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr1:165567000-165567400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:165567000-165567400	Flanking Active TSS	HepG2	liver
28	chr1:165567000-165567600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:165567000-165567600	Active TSS	GM12878-XiMat	blood
30	chr1:165567000-165567600	Active TSS	HUVEC	blood vessel
31	chr1:165567000-165567600	Active TSS	NH-A	brain
32	chr1:165567000-165567600	Active TSS	NHEK	skin
33	chr1:165567000-165567800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:165567000-165567800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:165567000-165567800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:165567000-165567800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:165567000-165567800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr1:165567000-165567800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:165567000-165567800	Active TSS	Adipose Nuclei	Adipose
40	chr1:165567000-165567800	Active TSS	Brain Anterior Caudate	brain
41	chr1:165567000-165567800	Active TSS	Brain Substantia Nigra	brain
42	chr1:165567000-165567800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr1:165567000-165567800	Active TSS	Fetal Stomach	stomach
44	chr1:165567000-165567800	Active TSS	Ovary	ovary
45	chr1:165567000-165567800	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:165567000-165567800	Active TSS	HSMM	muscle
47	chr1:165567000-165567800	Active TSS	NHDF-Ad	bronchial
48	chr1:165567000-165567800	Active TSS	NHLF	lung
49	chr1:165567000-165567800	Active TSS	Osteobl	bone
50	chr1:165567000-165568000	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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