Variant report

Variant	rs2255815
Chromosome Location	chr17:46049126-46049127
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	chr17:46047860-46049148	PANC-1	pancreas:	n/a	n/a
2	MAX	chr17:46047776-46049210	HCT-116	colon:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
3	SMARCB1	chr17:46047953-46049191	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr17:46048079-46049174	IMR90	lung:	n/a	n/a
5	SP1	chr17:46047685-46049130	A549	lung:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
6	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
7	MAX	chr17:46047592-46049187	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
8	POLR2A	chr17:46048258-46049145	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:46048048-46049181	K562	blood:	n/a	n/a
10	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a
11	MAX	chr17:46047865-46049183	ECC-1	luminal epithelium:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
12	TBP	chr17:46048011-46049185	K562	blood:	n/a	n/a
13	MAX	chr17:46047658-46049319	HCT-116	colon:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
14	FOSL2	chr17:46047768-46049187	A549	lung:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
15	E2F6	chr17:46047904-46049279	H1-hESC	embryonic stem cell:	n/a	chr17:46048715-46048726 chr17:46048296-46048308 chr17:46048717-46048724 chr17:46048373-46048382 chr17:46048717-46048724 chr17:46048716-46048725 chr17:46048717-46048724
16	CTCF	chr17:46047402-46049199	SK-N-SH	brain:	n/a	chr17:46048168-46048177
17	MAX	chr17:46047616-46049260	A549	lung:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
18	POLR2A	chr17:46047908-46049131	U87	brain:	n/a	n/a
19	MAX	chr17:46047736-46049186	ECC-1	luminal epithelium:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
20	MXI1	chr17:46047494-46049540	IMR90	lung:	n/a	n/a
21	MAX	chr17:46047925-46049219	MCF-7	breast:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
22	MAX	chr17:46047825-46049138	SK-N-SH	brain:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
23	SIN3AK20	chr17:46047317-46049226	MCF-7	breast:	n/a	n/a
24	NR2F2	chr17:46047840-46049590	K562	blood:	n/a	n/a
25	MAX	chr17:46047879-46049190	H1-hESC	embryonic stem cell:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
26	RAD21	chr17:46047598-46049158	SK-N-SH	brain:	n/a	chr17:46048248-46048258
27	E2F6	chr17:46047805-46049255	A549	lung:	n/a	chr17:46048715-46048726 chr17:46048296-46048308 chr17:46048717-46048724 chr17:46048373-46048382 chr17:46048717-46048724 chr17:46048716-46048725 chr17:46048717-46048724
28	MAX	chr17:46047653-46049233	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
29	MAX	chr17:46047701-46049131	MCF-7	breast:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
30	CTCF	chr17:46047393-46050115	A549	lung:	n/a	chr17:46048168-46048177
31	POLR2A	chr17:46047971-46049133	H1-hESC	embryonic stem cell:	n/a	n/a
32	GTF3C2	chr17:46048864-46049401	Hela-S3	cervix:	n/a	n/a
33	MAX	chr17:46047827-46049370	K562	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
34	RPC155	chr17:46048911-46049505	Hela-S3	cervix:	n/a	n/a
35	TCF12	chr17:46047510-46049280	A549	lung:	n/a	chr17:46048921-46048931 chr17:46048795-46048802
36	MAX	chr17:46047814-46049189	A549	lung:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
37	POLR2A	chr17:46047811-46049607	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
2	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
3	chr17:45915738..45918906-chr17:46047433..46049662,3	K562	blood:
4	chr17:46048621..46050545-chr17:46057076..46059668,3	K562	blood:
5	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
6	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
7	chr17:45971266..45974117-chr17:46049059..46051074,2	MCF-7	breast:
8	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
9	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
10	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
11	chr17:45727256..45728937-chr17:46047807..46049675,2	K562	blood:
12	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
13	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
14	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
15	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
16	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
17	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
18	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:
19	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
20	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000167182	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108424	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1476578	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1476579	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2003477	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2003478	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2255697	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525084	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525085	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525087	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525088	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525090	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525091	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525092	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525093	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525094	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2525096	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2525098	0.96[ASN][1000 genomes]
rs2597161	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2597165	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2597168	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597171	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2597172	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597173	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597174	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2597179	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2597180	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2597181	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2875746	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905845	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905846	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905848	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2905849	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2905850	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2905851	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2905852	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2905853	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34190379	0.93[ASN][1000 genomes]
rs35653190	0.82[ASN][1000 genomes]
rs62064873	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6503949	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs729785	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs729786	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs737130	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs739853	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7406338	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7503584	0.93[ASN][1000 genomes]
rs8076314	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885634	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 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	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum
2	chr17:46047400-46049200	Active TSS	Fetal Kidney	kidney
3	chr17:46047600-46049400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:46047600-46049600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:46047800-46049200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr17:46047800-46049200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:46047800-46049200	Active TSS	Psoas Muscle	Psoas
8	chr17:46047800-46049200	Active TSS	Right Atrium	heart
9	chr17:46047800-46049400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:46047800-46049400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr17:46047800-46050000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:46048000-46049200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr17:46048000-46049200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:46048000-46049200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:46048000-46049200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:46048000-46049200	Active TSS	Brain Angular Gyrus	brain
17	chr17:46048000-46049200	Active TSS	Brain Substantia Nigra	brain
18	chr17:46048000-46049200	Active TSS	Colon Smooth Muscle	Colon
19	chr17:46048000-46049200	Active TSS	Esophagus	oesophagus
20	chr17:46048000-46049200	Active TSS	Fetal Intestine Large	intestine
21	chr17:46048000-46049200	Active TSS	Fetal Intestine Small	intestine
22	chr17:46048000-46049200	Active TSS	Left Ventricle	heart
23	chr17:46048000-46049200	Active TSS	Lung	lung
24	chr17:46048000-46049200	Active TSS	NHLF	lung
25	chr17:46048000-46049400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr17:46048000-46049400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:46048000-46049400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr17:46048000-46049400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr17:46048000-46049400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:46048000-46049400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:46048000-46049400	Active TSS	Colonic Mucosa	Colon
32	chr17:46048000-46049400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr17:46048000-46049400	Active TSS	Ovary	ovary
34	chr17:46048000-46049400	Active TSS	GM12878-XiMat	blood
35	chr17:46048000-46049400	Active TSS	HSMM	muscle
36	chr17:46048000-46049400	Active TSS	NHDF-Ad	bronchial
37	chr17:46048000-46049600	Active TSS	HSMMtube	muscle
38	chr17:46048000-46049800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr17:46048200-46049200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:46048200-46049200	Active TSS	Muscle Satellite Cultured Cells	--
41	chr17:46048200-46049200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:46048200-46049200	Active TSS	Pancreas	Pancrea
43	chr17:46048200-46049200	Active TSS	A549	lung
44	chr17:46048200-46049200	Active TSS	HMEC	breast
45	chr17:46048200-46049200	Active TSS	K562	blood
46	chr17:46048200-46049200	Active TSS	NHEK	skin
47	chr17:46048400-46049200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:46048400-46049200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr17:46048400-46049200	Active TSS	Small Intestine	intestine
50	chr17:46048400-46049400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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