Variant report

Variant	rs2746072
Chromosome Location	chr1:192777807-192777808
allele	C/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	PBX3	chr1:192777533-192778881	SK-N-SH	brain:	n/a	n/a
2	HA-E2F1	chr1:192777358-192778875	MCF-7	breast:	n/a	chr1:192778120-192778129 chr1:192778331-192778343
3	MAX	chr1:192777156-192778721	Hela-S3	cervix:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
4	CTCF	chr1:192777760-192777910	GM12875	blood:	n/a	n/a
5	POLR2A	chr1:192777404-192778709	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF3	chr1:192777638-192778364	GM12878	blood:	n/a	chr1:192777927-192777940 chr1:192777923-192777937
7	MYC	chr1:192777618-192777994	MCF-7	breast:	n/a	n/a
8	CBX3	chr1:192777423-192778795	K562	blood:	n/a	n/a
9	POLR2A	chr1:192777515-192778670	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:192776886-192778449	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr1:192777740-192777890	NHEK	skin:	n/a	n/a
12	RAD21	chr1:192777647-192777963	HepG2	liver:	n/a	chr1:192777930-192777944
13	SMARCB1	chr1:192777183-192778957	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:192777480-192778598	Gliobla	brain:	n/a	n/a
15	CTCF	chr1:192777800-192777950	GM12871	blood:	n/a	n/a
16	CTCF	chr1:192777760-192777910	AG09319	gingival:	n/a	n/a
17	SIN3AK20	chr1:192777626-192778655	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr1:192777445-192778636	A549	lung:	n/a	n/a
19	GTF2F1	chr1:192777609-192778533	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:192777730-192778408	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr1:192777466-192778434	HepG2	liver:	n/a	n/a
22	CTCF	chr1:192777700-192777850	GM12872	blood:	n/a	n/a
23	TAF1	chr1:192777745-192778416	Hela-S3	cervix:	n/a	n/a
24	RFX5	chr1:192777732-192778701	Hela-S3	cervix:	n/a	n/a
25	TAF1	chr1:192777736-192778636	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr1:192777471-192778566	MCF-7	breast:	n/a	n/a
27	POLR2A	chr1:192777702-192778474	HUVEC	blood vessel:	n/a	n/a
28	CREB1	chr1:192777679-192778864	GM12878	blood:	n/a	n/a
29	MAX	chr1:192777140-192778716	K562	blood:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
30	POLR2A	chr1:192777757-192778683	GM12892	blood:	n/a	n/a
31	MAX	chr1:192777178-192778641	H1-hESC	embryonic stem cell:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
32	TAF1	chr1:192777406-192778865	H1-neurons	neurons:	n/a	n/a
33	TCF12	chr1:192777781-192778107	GM12878	blood:	n/a	chr1:192777937-192777944
34	E2F6	chr1:192777536-192778473	K562	blood:	n/a	chr1:192778120-192778129 chr1:192778331-192778343
35	FOSL2	chr1:192777509-192778299	A549	lung:	n/a	n/a
36	CREB1	chr1:192777697-192779018	K562	blood:	n/a	n/a
37	KAP1	chr1:192776513-192779169	HEK293	kidney:	n/a	chr1:192777251-192777259 chr1:192776622-192776631
38	MAX	chr1:192777490-192778583	ECC-1	luminal epithelium:	n/a	n/a
39	EP300	chr1:192777769-192778383	SK-N-SH_RA	brain:	n/a	chr1:192778035-192778051
40	MYC	chr1:192777676-192778747	NB4	blood:	n/a	n/a
41	PAX5	chr1:192777736-192778247	GM12878	blood:	n/a	chr1:192778024-192778033
42	MAZ	chr1:192777300-192778694	K562	blood:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
43	POLR2A	chr1:192777438-192778558	SK-N-MC	brain:	n/a	n/a
44	NR2F2	chr1:192777013-192778566	K562	blood:	n/a	chr1:192778435-192778450
45	POLR2A	chr1:192777662-192778436	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:192777127-192778871	Hela-S3	cervix:	n/a	n/a
47	MYC	chr1:192776444-192778399	MCF10A-Er-Src	breast:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777173-192777182 chr1:192777174-192777183 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354
48	ZNF143	chr1:192777406-192778462	H1-hESC	embryonic stem cell:	n/a	chr1:192777819-192777837
49	CTCF	chr1:192777740-192777890	MCF-7	breast:	n/a	n/a
50	MAX	chr1:192777324-192778574	ECC-1	luminal epithelium:	n/a	chr1:192777344-192777353 chr1:192777345-192777352 chr1:192777342-192777355 chr1:192777344-192777353 chr1:192777343-192777354 chr1:192777343-192777353 chr1:192777344-192777354

No.	Distal block	Cell Line	Cell type
1	chr1:192777340..192777996-chr17:20945690..20946550,2	Hela-S3	cervix:
2	chr1:192777388..192778329-chr17:1303225..1303741,2	Hela-S3	cervix:
3	chr1:192776599..192779563-chr1:193090962..193092551,2	K562	blood:
4	chr1:192775702..192778041-chr1:192986871..192988604,2	MCF-7	breast:
5	chr1:192775703..192778053-chr1:193028205..193029898,2	MCF-7	breast:
6	chr1:192773238..192775392-chr1:192775635..192777815,2	K562	blood:
7	chr1:192459062..192461935-chr1:192775675..192778515,2	K562	blood:
8	chr1:192777718..192778346-chr19:14628685..14629446,2	Hela-S3	cervix:
9	chr1:192777538..192778505-chr7:65540311..65541089,2	Hela-S3	cervix:
10	chr1:192777293..192779700-chr1:193028238..193029983,2	K562	blood:
11	chr1:192777305..192779700-chr1:193027165..193029983,2	K562	blood:
12	chr1:156561359..156562120-chr1:192777716..192778276,2	HCT-116	colon:

Variant related genes	Relation type
RGS2	TF binding region
ENSG00000124422	Chromatin interaction
ENSG00000126522	Chromatin interaction
ENSG00000108953	Chromatin interaction
ENSG00000163382	Chromatin interaction
ENSG00000134371	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000116750	Chromatin interaction
ENSG00000221145	Chromatin interaction
ENSG00000116747	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10737617	0.82[ASN][1000 genomes]
rs10737618	0.91[ASN][1000 genomes]
rs10754031	0.91[ASN][1000 genomes]
rs10801151	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10801152	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10801153	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10801154	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10801156	0.98[EUR][1000 genomes]
rs10801157	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10801158	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10921265	0.91[ASN][1000 genomes]
rs10921267	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10921268	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586572	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565835	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418718	0.92[EUR][1000 genomes]
rs16834851	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1819741	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1933694	0.82[ASN][1000 genomes]
rs2746071	0.93[EUR][1000 genomes]
rs2746073	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856223	0.88[ASN][1000 genomes]
rs4128057	0.82[ASN][1000 genomes]
rs6428136	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6669632	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670129	0.82[ASN][1000 genomes]
rs6670801	0.83[ASN][1000 genomes]
rs6670806	0.83[ASN][1000 genomes]
rs6684156	0.92[EUR][1000 genomes]
rs6703040	0.83[AFR][1000 genomes]
rs7525778	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546861	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549721	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192775800-192778200	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:192776000-192778800	Active TSS	Colon Smooth Muscle	Colon
3	chr1:192776200-192780600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:192776400-192779400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr1:192776400-192779400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:192776400-192779600	Active TSS	Brain Cingulate Gyrus	brain
7	chr1:192776400-192779800	Active TSS	Ovary	ovary
8	chr1:192776400-192779800	Active TSS	Stomach Mucosa	stomach
9	chr1:192776400-192780600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:192776400-192780600	Active TSS	Aorta	Aorta
11	chr1:192776400-192781200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:192776600-192779800	Active TSS	Colonic Mucosa	Colon
13	chr1:192776800-192779600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:192777000-192780000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:192777000-192781200	ZNF genes & repeats	Fetal Brain Male	brain
16	chr1:192777200-192778000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:192777200-192778200	Active TSS	Brain Germinal Matrix	brain
18	chr1:192777200-192778200	Flanking Active TSS	Dnd41	blood
19	chr1:192777200-192778600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:192777200-192779400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:192777200-192779400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:192777200-192779400	Active TSS	Fetal Brain Female	brain
23	chr1:192777200-192779800	Active TSS	Pancreas	Pancrea
24	chr1:192777200-192780000	Active TSS	Fetal Muscle Trunk	muscle
25	chr1:192777400-192778000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:192777400-192778000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:192777400-192778000	Flanking Active TSS	HMEC	breast
28	chr1:192777400-192778600	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:192777400-192778800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:192777400-192778800	Active TSS	Duodenum Mucosa	Duodenum
31	chr1:192777400-192779000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:192777400-192779000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:192777400-192779000	Active TSS	Gastric	stomach
34	chr1:192777400-192779200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:192777400-192779400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:192777400-192779400	Active TSS	Brain Anterior Caudate	brain
37	chr1:192777400-192779400	Active TSS	Esophagus	oesophagus
38	chr1:192777400-192779400	Active TSS	Left Ventricle	heart
39	chr1:192777400-192779600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:192777400-192779600	Active TSS	Small Intestine	intestine
41	chr1:192777400-192779600	Active TSS	NHDF-Ad	bronchial
42	chr1:192777400-192779800	Active TSS	Brain Substantia Nigra	brain
43	chr1:192777400-192779800	Active TSS	Placenta Amnion	Placenta Amnion
44	chr1:192777400-192779800	Active TSS	Right Ventricle	heart
45	chr1:192777600-192778000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:192777600-192778000	Transcr. at gene 5' and 3'	Right Atrium	heart
47	chr1:192777600-192778200	Active TSS	Primary B cells from cord blood	blood
48	chr1:192777600-192778200	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr1:192777600-192778400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:192777600-192778400	Active TSS	Primary T cells from cord blood	blood

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