Variant report

Variant	rs6427628
Chromosome Location	chr1:161735397-161735398
allele	A/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	SIN3AK20	chr1:161735010-161735429	A549	lung:	n/a	n/a
2	SP1	chr1:161734682-161735556	HCT-116	colon:	n/a	n/a
3	FOSL1	chr1:161734917-161735498	HCT-116	colon:	n/a	n/a
4	MAX	chr1:161734886-161735474	MCF-7	breast:	n/a	n/a
5	ARID3A	chr1:161734867-161736503	HepG2	liver:	n/a	n/a
6	MXI1	chr1:161734401-161736955	SK-N-SH	brain:	n/a	n/a
7	TAF1	chr1:161735026-161735405	PFSK-1	brain:	n/a	n/a
8	ELK1	chr1:161735036-161735437	Hela-S3	cervix:	n/a	n/a
9	MAX	chr1:161734626-161735555	HCT-116	colon:	n/a	n/a
10	FOSL1	chr1:161734902-161735638	HCT-116	colon:	n/a	n/a
11	ZNF143	chr1:161735050-161735417	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:161735009-161736873	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:161734890-161735445	SK-N-MC	brain:	n/a	n/a
14	MAX	chr1:161734940-161735458	MCF-7	breast:	n/a	n/a
15	SIN3AK20	chr1:161734999-161735437	PANC-1	pancreas:	n/a	n/a
16	CUX1	chr1:161735065-161736312	GM12878	blood:	n/a	n/a
17	KAP1	chr1:161734876-161735443	HEK293	kidney:	n/a	n/a
18	POLR2A	chr1:161734903-161735509	SK-N-MC	brain:	n/a	n/a
19	MAX	chr1:161734798-161736695	A549	lung:	n/a	n/a
20	E2F4	chr1:161735136-161735475	GM12878	blood:	n/a	n/a
21	BRCA1	chr1:161734945-161735417	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr1:161734965-161735409	MCF-7	breast:	n/a	chr1:161735142-161735153
23	STAT3	chr1:161734954-161735400	MCF10A-Er-Src	breast:	n/a	chr1:161735184-161735195
24	EGR1	chr1:161734798-161735497	HCT-116	colon:	n/a	n/a
25	FOXM1	chr1:161734910-161735658	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr1:161734888-161735513	ECC-1	luminal epithelium:	n/a	n/a
27	STAT3	chr1:161734954-161735464	MCF10A-Er-Src	breast:	n/a	chr1:161735421-161735444 chr1:161735184-161735195
28	POLR2A	chr1:161734908-161735521	HCT-116	colon:	n/a	n/a
29	EP300	chr1:161734988-161736153	Hela-S3	cervix:	n/a	chr1:161736096-161736105 chr1:161735550-161735560
30	ZNF384	chr1:161735339-161735437	GM12878	blood:	n/a	n/a
31	IRF1	chr1:161735070-161736328	K562	blood:	n/a	chr1:161735311-161735327
32	MAX	chr1:161734949-161735478	Hela-S3	cervix:	n/a	n/a
33	CREB1	chr1:161734913-161735465	HepG2	liver:	n/a	n/a
34	SP1	chr1:161734999-161735462	H1-hESC	embryonic stem cell:	n/a	n/a
35	MXI1	chr1:161734981-161735437	Hela-S3	cervix:	n/a	n/a
36	ZNF143	chr1:161735052-161735412	GM12878	blood:	n/a	n/a
37	MYBL2	chr1:161734912-161735452	HepG2	liver:	n/a	n/a
38	ARID3A	chr1:161735047-161735455	K562	blood:	n/a	n/a
39	PBX3	chr1:161734804-161735428	SK-N-SH	brain:	n/a	n/a
40	SETDB1	chr1:161734921-161735469	U2OS	brain:	n/a	n/a
41	CEBPB	chr1:161734895-161735498	A549	lung:	n/a	chr1:161735142-161735153
42	STAT3	chr1:161734947-161735474	MCF10A-Er-Src	breast:	n/a	chr1:161735421-161735444 chr1:161735184-161735195
43	POLR2A	chr1:161735036-161735449	GM12878	blood:	n/a	n/a
44	GTF3C2	chr1:161734588-161735433	Hela-S3	cervix:	n/a	n/a
45	MXI1	chr1:161734866-161736880	IMR90	lung:	n/a	n/a
46	CHD1	chr1:161735041-161736736	GM12878	blood:	n/a	n/a
47	E2F4	chr1:161735066-161735529	MCF10A-Er-Src	breast:	n/a	n/a
48	MXI1	chr1:161734987-161735397	HepG2	liver:	n/a	n/a
49	EP300	chr1:161734992-161735507	K562	blood:	n/a	n/a
50	TEAD4	chr1:161734928-161735401	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
2	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
3	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:

Variant related genes	Relation type
ATF6	TF binding region
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2340717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2340719	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2340722	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2341472	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2490425	0.91[EUR][1000 genomes]
rs2490426	0.91[EUR][1000 genomes]
rs2490427	0.93[EUR][1000 genomes]
rs2490429	0.95[EUR][1000 genomes]
rs2997506	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4233381	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4657094	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4657095	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4657111	0.90[AMR][1000 genomes]
rs6687226	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
2	chr1:161723400-161736000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:161724600-161736000	Weak transcription	Small Intestine	intestine
4	chr1:161724800-161736000	Weak transcription	Gastric	stomach
5	chr1:161726000-161735800	Weak transcription	Esophagus	oesophagus
6	chr1:161726800-161735800	Weak transcription	Lung	lung
7	chr1:161728600-161736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:161728800-161735400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:161733600-161737000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:161733800-161737400	Active TSS	A549	lung
11	chr1:161734000-161735800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:161734400-161736000	Active TSS	HepG2	liver
13	chr1:161734600-161735400	Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:161734600-161735800	Active TSS	Brain Germinal Matrix	brain
15	chr1:161734600-161736000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:161734600-161736000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:161734600-161736200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:161734600-161736400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:161734600-161736400	Active TSS	Adipose Nuclei	Adipose
20	chr1:161734600-161736400	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:161734600-161736400	Active TSS	Hela-S3	cervix
22	chr1:161734600-161736600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr1:161734600-161736600	Active TSS	Placenta	Placenta
24	chr1:161734600-161736600	Active TSS	Rectal Smooth Muscle	rectum
25	chr1:161734600-161736600	Active TSS	Right Atrium	heart
26	chr1:161734600-161736600	Active TSS	NH-A	brain
27	chr1:161734600-161736800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:161734600-161736800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:161734600-161736800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:161734600-161736800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:161734600-161736800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:161734600-161736800	Active TSS	Fetal Intestine Large	intestine
33	chr1:161734600-161736800	Active TSS	Fetal Kidney	kidney
34	chr1:161734600-161736800	Active TSS	Fetal Muscle Leg	muscle
35	chr1:161734600-161736800	Active TSS	Fetal Stomach	stomach
36	chr1:161734600-161736800	Active TSS	HSMM	muscle
37	chr1:161734600-161736800	Active TSS	HSMMtube	muscle
38	chr1:161734600-161736800	Active TSS	HUVEC	blood vessel
39	chr1:161734600-161736800	Active TSS	NHDF-Ad	bronchial
40	chr1:161734600-161736800	Active TSS	NHEK	skin
41	chr1:161734600-161737000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr1:161734600-161737000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr1:161734600-161737000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:161734600-161737000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr1:161734600-161737000	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:161734600-161737000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:161734600-161737000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:161734600-161737000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:161734600-161737000	Active TSS	Aorta	Aorta
50	chr1:161734600-161737000	Active TSS	Pancreatic Islets	Pancreatic Islet

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