Variant report

Variant	rs17040781
Chromosome Location	chr4:110624836-110624837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:196)
CpG islands
(count:122)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:196 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr4:110624059-110624949	ECC-1	luminal epithelium:	n/a	chr4:110624275-110624294
2	TCF7L2	chr4:110624130-110624956	HCT-116	colon:	n/a	n/a
3	TAF1	chr4:110624075-110624853	K562	blood:	n/a	n/a
4	POLR2A	chr4:110624043-110624979	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr4:110623065-110625373	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:110624079-110625113	HL-60	blood:	n/a	n/a
7	TBP	chr4:110623746-110624953	K562	blood:	n/a	n/a
8	E2F6	chr4:110624099-110624910	K562	blood:	n/a	chr4:110624251-110624261 chr4:110624322-110624331 chr4:110624323-110624330 chr4:110624323-110624330 chr4:110624323-110624330 chr4:110624687-110624696 chr4:110624777-110624787 chr4:110624252-110624262
9	RCOR1	chr4:110624097-110624972	K562	blood:	n/a	n/a
10	POLR2A	chr4:110623689-110624995	GM18505	blood:	n/a	n/a
11	POLR2A	chr4:110623748-110624957	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr4:110622699-110625610	H1-hESC	embryonic stem cell:	n/a	n/a
13	ATF2	chr4:110624301-110624850	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr4:110624655-110624921	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr4:110624678-110624900	HepG2	liver:	n/a	n/a
16	ELF1	chr4:110624368-110625033	MCF-7	breast:	n/a	chr4:110624753-110624765
17	POLR2A	chr4:110624036-110624884	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr4:110624089-110625161	MCF-7	breast:	n/a	n/a
19	POLR2A	chr4:110624325-110625007	PANC-1	pancreas:	n/a	n/a
20	EP300	chr4:110624778-110624933	K562	blood:	n/a	n/a
21	POLR2A	chr4:110624091-110625314	K562	blood:	n/a	n/a
22	HEY1	chr4:110624357-110624914	K562	blood:	n/a	chr4:110624689-110624704
23	POLR2A	chr4:110624275-110625093	HepG2	liver:	n/a	n/a
24	JUN	chr4:110623696-110625065	K562	blood:	n/a	chr4:110624053-110624065
25	POLR2A	chr4:110624164-110624882	GM12878	blood:	n/a	n/a
26	HDAC2	chr4:110624058-110624978	MCF-7	breast:	n/a	chr4:110624100-110624109
27	POLR2A	chr4:110624245-110624943	Gliobla	brain:	n/a	n/a
28	BCLAF1	chr4:110623560-110625057	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:110624119-110625134	HCT-116	colon:	n/a	n/a
30	CTCF	chr4:110624740-110624890	GM12864	blood:	n/a	chr4:110624854-110624863
31	PML	chr4:110624198-110624837	MCF-7	breast:	n/a	n/a
32	ELF1	chr4:110623828-110625003	GM12878	blood:	n/a	chr4:110624753-110624765
33	POLR2A	chr4:110623590-110624980	GM18951	blood:	n/a	n/a
34	POLR2A	chr4:110624081-110624970	NB4	blood:	n/a	n/a
35	MAZ	chr4:110623824-110625166	GM12878	blood:	n/a	n/a
36	NFATC1	chr4:110624366-110625157	GM12878	blood:	n/a	n/a
37	SMC3	chr4:110623776-110625919	SK-N-SH	brain:	n/a	chr4:110624276-110624290 chr4:110624280-110624290
38	POLR2A	chr4:110624147-110624940	MCF-7	breast:	n/a	n/a
39	POLR2A	chr4:110624082-110625147	Hela-S3	cervix:	n/a	n/a
40	UBTF	chr4:110623825-110624844	K562	blood:	n/a	n/a
41	CTBP2	chr4:110624115-110624857	H1-hESC	embryonic stem cell:	n/a	n/a
42	MYC	chr4:110623793-110624987	NB4	blood:	n/a	n/a
43	TBP	chr4:110623819-110624993	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:110624292-110624911	A549	lung:	n/a	n/a
45	TCF12	chr4:110624075-110624996	ECC-1	luminal epithelium:	n/a	chr4:110624139-110624146 chr4:110624930-110624940 chr4:110624100-110624109
46	FOXP2	chr4:110624405-110624895	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr4:110624045-110625405	K562	blood:	n/a	n/a
48	ZNF143	chr4:110623771-110624900	GM12878	blood:	n/a	chr4:110624252-110624262 chr4:110624777-110624787 chr4:110624251-110624261
49	POLR2A	chr4:110624709-110624918	HepG2	liver:	n/a	n/a
50	POLR2A	chr4:110623853-110625277	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:110624798-110624848	IMR90	lung:	fetal
2	chr4:110624798-110624848	LNCaP	prostate:	n/a
3	chr4:110624796-110624846	BJ	skin:	n/a
4	chr4:110624796-110624846	HCT-116	colon:	n/a
5	chr4:110624798-110624848	HEEpiC	esophagus:	n/a
6	chr4:110624796-110624846	HRE	kidney:	n/a
7	chr4:110624798-110624848	Jurkat	blood:	n/a
8	chr4:110624796-110624846	RPTEC	kidney:	n/a
9	chr4:110624798-110624848	AG04449	skin:	fetal
10	chr4:110624796-110624846	GM12891	blood:	n/a
11	chr4:110624798-110624848	SK-N-SH_RA	brain:	n/a
12	chr4:110624796-110624846	SK-N-SH_RA	brain:	n/a
13	chr4:110624796-110624846	A549	lung:	n/a
14	chr4:110624798-110624848	BE2_C	brain:	n/a
15	chr4:110624796-110624846	SAEC	small airway:	n/a
16	chr4:110624796-110624846	SK-N-SH	brain:	n/a
17	chr4:110624798-110624848	AG04450	lung:	fetal
18	chr4:110624796-110624846	Hepatocyte	liver:	n/a
19	chr4:110624798-110624848	H1-hESC	embryonic stem cell:	embryo
20	chr4:110624796-110624846	HPAEpiC	pulmonary alveolar:	n/a
21	chr4:110624798-110624848	AG09309	skin:	n/a
22	chr4:110624798-110624848	GM12892	blood:	n/a
23	chr4:110624798-110624848	HMEC	breast:	n/a
24	chr4:110624796-110624846	Hela-S3	cervix:	n/a
25	chr4:110624796-110624846	ECC-1	luminal epithelium:	n/a
26	chr4:110624798-110624848	T-47D	breast:	n/a
27	chr4:110624796-110624846	AoSMC	blood vessel:	n/a
28	chr4:110624796-110624846	HMEC	breast:	n/a
29	chr4:110624796-110624846	HNPCEpiC	eye:	n/a
30	chr4:110624798-110624848	HEK293	kidney:	embryo
31	chr4:110624796-110624846	AG04449	skin:	fetal
32	chr4:110624798-110624848	HRCEpiC	kidney:	n/a
33	chr4:110624798-110624848	HL-60	blood:	n/a
34	chr4:110624798-110624848	Hepatocyte	liver:	n/a
35	chr4:110624798-110624848	ProgFib	skin:	n/a
36	chr4:110624798-110624848	Hela-S3	cervix:	n/a
37	chr4:110624798-110624848	SK-N-MC	brain:	n/a
38	chr4:110624796-110624846	NH-A	brain:	n/a
39	chr4:110624798-110624848	AG09319	gingival:	n/a
40	chr4:110624796-110624846	HRCEpiC	kidney:	n/a
41	chr4:110624798-110624848	SKMC	muscle:	n/a
42	chr4:110624798-110624848	MCF10A-Er-Src	breast:	n/a
43	chr4:110624796-110624846	AG10803	skin:	n/a
44	chr4:110624796-110624846	GM12878	blood:	n/a
45	chr4:110624798-110624848	SAEC	small airway:	n/a
46	chr4:110624798-110624848	HRE	kidney:	n/a
47	chr4:110624798-110624848	A549	lung:	n/a
48	chr4:110624796-110624846	HCM	heart:	n/a
49	chr4:110624796-110624846	AG04450	lung:	fetal
50	chr4:110624798-110624848	MCF-7	breast:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:110622125..110626663-chr4:110647059..110653148,13	MCF-7	breast:
2	chr4:110621753..110625851-chr4:110723328..110725382,3	MCF-7	breast:
3	chr4:110623968..110625956-chr4:110651024..110652981,2	MCF-7	breast:
4	chr4:110614175..110617352-chr4:110621711..110624911,3	K562	blood:
5	chr4:110618563..110622220-chr4:110622548..110625878,6	K562	blood:
6	chr4:110622297..110625771-chr4:110735143..110738902,5	K562	blood:
7	chr4:110623136..110625842-chr4:110784972..110787630,2	MCF-7	breast:
8	chr4:110622109..110625008-chr4:110733953..110738254,7	MCF-7	breast:

No data

Variant related genes	Relation type
CASP6	TF binding region
CASP6	CpG island
ENSG00000138794	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000183423	Chromatin interaction
ENSG00000123739	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3733612	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796910	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030541	1.00[EUR][1000 genomes]
rs5030543	1.00[EUR][1000 genomes]
rs5030545	1.00[EUR][1000 genomes]
rs5030560	1.00[EUR][1000 genomes]
rs58686153	1.00[EUR][1000 genomes]
rs59712566	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60473457	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61164442	1.00[EUR][1000 genomes];1.00[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	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:110622600-110625000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr4:110622800-110625000	Active TSS	Brain Hippocampus Middle	brain
3	chr4:110622800-110625200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:110622800-110625200	Active TSS	Fetal Intestine Large	intestine
5	chr4:110623000-110625000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:110623000-110625000	Active TSS	HepG2	liver
7	chr4:110623000-110625200	Active TSS	Fetal Kidney	kidney
8	chr4:110623000-110625200	Active TSS	NH-A	brain
9	chr4:110623200-110625000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:110623200-110625000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:110623200-110625000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:110623200-110625000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:110623200-110625000	Active TSS	Placenta Amnion	Placenta Amnion
14	chr4:110623200-110625000	Active TSS	Psoas Muscle	Psoas
15	chr4:110623200-110625200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr4:110623200-110625200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr4:110623200-110625400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr4:110623200-110625400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:110623400-110625000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:110623400-110625000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:110623400-110625000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:110623400-110625000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:110623400-110625000	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr4:110623400-110625000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:110623400-110625000	Active TSS	Brain Angular Gyrus	brain
26	chr4:110623400-110625000	Active TSS	Brain Anterior Caudate	brain
27	chr4:110623400-110625000	Active TSS	Esophagus	oesophagus
28	chr4:110623400-110625000	Active TSS	Fetal Intestine Small	intestine
29	chr4:110623400-110625000	Active TSS	Fetal Lung	lung
30	chr4:110623400-110625000	Active TSS	Gastric	stomach
31	chr4:110623400-110625000	Active TSS	Left Ventricle	heart
32	chr4:110623400-110625000	Active TSS	Pancreas	Pancrea
33	chr4:110623400-110625000	Active TSS	Small Intestine	intestine
34	chr4:110623400-110625000	Active TSS	HSMMtube	muscle
35	chr4:110623400-110625200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr4:110623400-110625200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:110623400-110625200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr4:110623400-110625200	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr4:110623400-110625200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:110623400-110625200	Active TSS	Ovary	ovary
41	chr4:110623400-110625200	Active TSS	Rectal Smooth Muscle	rectum
42	chr4:110623400-110625200	Active TSS	Right Ventricle	heart
43	chr4:110623400-110625200	Active TSS	NHDF-Ad	bronchial
44	chr4:110623400-110625400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:110623400-110625400	Active TSS	Colonic Mucosa	Colon
46	chr4:110623400-110625400	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr4:110623400-110625400	Active TSS	Right Atrium	heart
48	chr4:110623400-110625400	Active TSS	Stomach Mucosa	stomach
49	chr4:110623600-110625000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:110623600-110625000	Active TSS	Liver	Liver

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