Variant report

Variant	rs3181340
Chromosome Location	chr4:110624021-110624022
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	chr4:110623065-110625373	GM12891	blood:	n/a	n/a
2	TBP	chr4:110623746-110624953	K562	blood:	n/a	n/a
3	POLR2A	chr4:110623689-110624995	GM18505	blood:	n/a	n/a
4	POLR2A	chr4:110623748-110624957	HUVEC	blood vessel:	n/a	n/a
5	TAF1	chr4:110623547-110624731	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:110622699-110625610	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr4:110623669-110624479	GM12878	blood:	n/a	n/a
8	YY1	chr4:110623965-110624832	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXM1	chr4:110623618-110624736	GM12878	blood:	n/a	n/a
10	CHD1	chr4:110623684-110624488	H1-hESC	embryonic stem cell:	n/a	n/a
11	JUN	chr4:110623696-110625065	K562	blood:	n/a	chr4:110624053-110624065
12	BCLAF1	chr4:110623560-110625057	GM12878	blood:	n/a	n/a
13	TRIM28	chr4:110623721-110624418	K562	blood:	n/a	n/a
14	TCF3	chr4:110623869-110624626	GM12878	blood:	n/a	n/a
15	EP300	chr4:110623838-110624330	GM12878	blood:	n/a	chr4:110623942-110623956 chr4:110624253-110624262
16	SP1	chr4:110623794-110624470	GM12878	blood:	n/a	n/a
17	ELF1	chr4:110623828-110625003	GM12878	blood:	n/a	chr4:110624753-110624765
18	POLR2A	chr4:110623590-110624980	GM18951	blood:	n/a	n/a
19	ETS1	chr4:110623796-110624182	GM12878	blood:	n/a	n/a
20	YY1	chr4:110623988-110624377	GM12891	blood:	n/a	n/a
21	WRNIP1	chr4:110623766-110624496	GM12878	blood:	n/a	n/a
22	MAZ	chr4:110623824-110625166	GM12878	blood:	n/a	n/a
23	CTCF	chr4:110623980-110624130	AoAF	blood vessel:	n/a	n/a
24	SMC3	chr4:110623776-110625919	SK-N-SH	brain:	n/a	chr4:110624276-110624290 chr4:110624280-110624290
25	UBTF	chr4:110623825-110624844	K562	blood:	n/a	n/a
26	FOXM1	chr4:110623721-110624458	GM12878	blood:	n/a	n/a
27	MXI1	chr4:110624009-110624783	Hela-S3	cervix:	n/a	n/a
28	MXI1	chr4:110623789-110624512	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr4:110623801-110624668	A549	lung:	n/a	chr4:110624277-110624290 chr4:110624274-110624292 chr4:110624277-110624290 chr4:110624275-110624291 chr4:110624280-110624293
30	MYC	chr4:110623793-110624987	NB4	blood:	n/a	n/a
31	TBP	chr4:110623819-110624993	H1-hESC	embryonic stem cell:	n/a	n/a
32	MEF2A	chr4:110623846-110624414	GM12878	blood:	n/a	n/a
33	BATF	chr4:110623894-110624217	GM12878	blood:	n/a	n/a
34	CTCF	chr4:110623824-110624540	IMR90	lung:	n/a	chr4:110624277-110624290 chr4:110624274-110624292 chr4:110624277-110624290 chr4:110624275-110624291 chr4:110624280-110624293
35	POLR2A	chr4:110623864-110624391	GM12878	blood:	n/a	n/a
36	ZNF143	chr4:110623771-110624900	GM12878	blood:	n/a	chr4:110624252-110624262 chr4:110624777-110624787 chr4:110624251-110624261
37	POLR2A	chr4:110623853-110625277	K562	blood:	n/a	n/a
38	POLR2A	chr4:110623848-110625598	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr4:110624008-110624595	MCF-7	breast:	n/a	chr4:110624277-110624290 chr4:110624274-110624292 chr4:110624277-110624290 chr4:110624275-110624291 chr4:110624280-110624293
40	RUNX3	chr4:110623584-110624933	GM12878	blood:	n/a	chr4:110623898-110623907 chr4:110623898-110623907
41	SRF	chr4:110623938-110624309	GM12878	blood:	n/a	chr4:110624175-110624186
42	RAD21	chr4:110623737-110624518	IMR90	lung:	n/a	chr4:110624275-110624294 chr4:110623973-110623987
43	CTCF	chr4:110624016-110624497	K562	blood:	n/a	chr4:110624277-110624290 chr4:110624274-110624292 chr4:110624277-110624290 chr4:110624275-110624291 chr4:110624280-110624293
44	RAD21	chr4:110623970-110624438	GM12878	blood:	n/a	chr4:110624275-110624294 chr4:110623973-110623987
45	CTCF	chr4:110623809-110624839	GM12878	blood:	n/a	chr4:110624737-110624750 chr4:110624277-110624290 chr4:110624274-110624292 chr4:110624277-110624290 chr4:110624275-110624291 chr4:110624280-110624293
46	CEBPB	chr4:110623782-110624517	GM12878	blood:	n/a	n/a
47	EP300	chr4:110623883-110624499	GM12878	blood:	n/a	chr4:110623942-110623956 chr4:110624253-110624262
48	YY1	chr4:110623902-110624448	GM12891	blood:	n/a	n/a
49	POLR2A	chr4:110623739-110625267	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr4:110623756-110625130	PBDE	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:110623974-110624024	HL-60	blood:	n/a
2	chr4:110623974-110624024	NH-A	brain:	n/a
3	chr4:110623974-110624024	MCF10A-Er-Src	breast:	n/a
4	chr4:110623974-110624024	HPAEpiC	pulmonary alveolar:	n/a
5	chr4:110623974-110624024	AG04450	lung:	fetal
6	chr4:110623974-110624024	NHDF-neo	bronchial:	n/a
7	chr4:110623974-110624024	HEK293	kidney:	embryo
8	chr4:110623974-110624024	ProgFib	skin:	n/a
9	chr4:110623974-110624024	HRCEpiC	kidney:	n/a
10	chr4:110623974-110624024	GM12878	blood:	n/a
11	chr4:110623974-110624024	BJ	skin:	n/a
12	chr4:110623974-110624024	ECC-1	luminal epithelium:	n/a
13	chr4:110623974-110624024	ovcar-3	ovarian:	n/a
14	chr4:110623974-110624024	GM12891	blood:	n/a
15	chr4:110623974-110624024	RPTEC	kidney:	n/a
16	chr4:110623974-110624024	Hela-S3	cervix:	n/a
17	chr4:110623974-110624024	BE2_C	brain:	n/a
18	chr4:110623974-110624024	AG04449	skin:	fetal
19	chr4:110623974-110624024	HCF	heart:	n/a
20	chr4:110623974-110624024	SAEC	small airway:	n/a
21	chr4:110623974-110624024	AG09309	skin:	n/a
22	chr4:110623974-110624024	PFSK-1	brain:	n/a
23	chr4:110623974-110624024	AG09319	gingival:	n/a
24	chr4:110623974-110624024	MCF-7	breast:	n/a
25	chr4:110623974-110624024	NT2-D1	testis:	n/a
26	chr4:110623974-110624024	SKMC	muscle:	n/a
27	chr4:110623974-110624024	AoSMC	blood vessel:	n/a
28	chr4:110623974-110624024	A549	lung:	n/a
29	chr4:110623974-110624024	AG10803	skin:	n/a
30	chr4:110623974-110624024	GM12892	blood:	n/a
31	chr4:110623974-110624024	T-47D	breast:	n/a
32	chr4:110623974-110624024	NB4	blood:	n/a
33	chr4:110623974-110624024	CMK	blood:	n/a
34	chr4:110623974-110624024	HEEpiC	esophagus:	n/a
35	chr4:110623974-110624024	SK-N-SH	brain:	n/a
36	chr4:110623974-110624024	GM06990	blood:	n/a
37	chr4:110623974-110624024	Caco-2	colon:	n/a
38	chr4:110623974-110624024	HRE	kidney:	n/a
39	chr4:110623974-110624024	SK-N-MC	brain:	n/a
40	chr4:110623974-110624024	HMEC	breast:	n/a
41	chr4:110623974-110624024	HCPEpiC	choroid plexus:	n/a
42	chr4:110623974-110624024	NHBE	bronchial:	n/a
43	chr4:110623974-110624024	LNCaP	prostate:	n/a
44	chr4:110623974-110624024	GM19239	blood:	n/a
45	chr4:110623974-110624024	SK-N-SH_RA	brain:	n/a
46	chr4:110623974-110624024	HCT-116	colon:	n/a
47	chr4:110623974-110624024	H1-hESC	embryonic stem cell:	embryo
48	chr4:110623974-110624024	Jurkat	blood:	n/a
49	chr4:110623974-110624024	HepG2	liver:	n/a
50	chr4:110623974-110624024	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:110622125..110626663-chr4:110647059..110653148,13	MCF-7	breast:
2	chr1:11967066..11969049-chr4:110623162..110624730,2	MCF-7	breast:
3	chr4:110621753..110625851-chr4:110723328..110725382,3	MCF-7	breast:
4	chr4:110623968..110625956-chr4:110651024..110652981,2	MCF-7	breast:
5	chr4:110617659..110620407-chr4:110623274..110624827,2	MCF-7	breast:
6	chr4:110614175..110617352-chr4:110621711..110624911,3	K562	blood:
7	chr4:110621463..110624410-chr4:110832783..110835223,2	K562	blood:
8	chr4:110618563..110622220-chr4:110622548..110625878,6	K562	blood:
9	chr4:110622297..110625771-chr4:110735143..110738902,5	K562	blood:
10	chr4:110621787..110624443-chr4:110734368..110736643,3	K562	blood:
11	chr4:110611889..110614128-chr4:110622707..110624451,2	MCF-7	breast:
12	chr4:110623136..110625842-chr4:110784972..110787630,2	MCF-7	breast:
13	chr4:110622109..110625008-chr4:110733953..110738254,7	MCF-7	breast:

Variant related genes	Relation type
CASP6	TF binding region
CASP6	CpG island
ENSG00000273447	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000183423	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000138798	Chromatin interaction
ENSG00000138794	Chromatin interaction
ENSG00000109534	Chromatin interaction
ENSG00000123739	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs5030522	0.98[AFR][1000 genomes]
rs5030525	0.98[AFR][1000 genomes]
rs5030527	0.98[AFR][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	chr4:110623000-110624200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:110623000-110625000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:110623000-110625000	Active TSS	HepG2	liver
8	chr4:110623000-110625200	Active TSS	Fetal Kidney	kidney
9	chr4:110623000-110625200	Active TSS	NH-A	brain
10	chr4:110623200-110625000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:110623200-110625000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:110623200-110625000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:110623200-110625000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:110623200-110625000	Active TSS	Placenta Amnion	Placenta Amnion
15	chr4:110623200-110625000	Active TSS	Psoas Muscle	Psoas
16	chr4:110623200-110625200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:110623200-110625200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr4:110623200-110625400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr4:110623200-110625400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr4:110623400-110624600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr4:110623400-110624600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:110623400-110624600	Active TSS	HMEC	breast
23	chr4:110623400-110624800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:110623400-110624800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:110623400-110624800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr4:110623400-110624800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr4:110623400-110624800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:110623400-110624800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:110623400-110624800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:110623400-110624800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:110623400-110624800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:110623400-110624800	Active TSS	Brain Cingulate Gyrus	brain
33	chr4:110623400-110624800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:110623400-110624800	Active TSS	Thymus	Thymus
35	chr4:110623400-110624800	Active TSS	GM12878-XiMat	blood
36	chr4:110623400-110624800	Active TSS	Hela-S3	cervix
37	chr4:110623400-110624800	Active TSS	HUVEC	blood vessel
38	chr4:110623400-110624800	Active TSS	NHLF	lung
39	chr4:110623400-110625000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:110623400-110625000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:110623400-110625000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr4:110623400-110625000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:110623400-110625000	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr4:110623400-110625000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:110623400-110625000	Active TSS	Brain Angular Gyrus	brain
46	chr4:110623400-110625000	Active TSS	Brain Anterior Caudate	brain
47	chr4:110623400-110625000	Active TSS	Esophagus	oesophagus
48	chr4:110623400-110625000	Active TSS	Fetal Intestine Small	intestine
49	chr4:110623400-110625000	Active TSS	Fetal Lung	lung
50	chr4:110623400-110625000	Active TSS	Gastric	stomach

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