Variant report

Variant	rs17839118
Chromosome Location	chr4:120222267-120222268
allele	A/C
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	MBD4	chr4:120221316-120222289	HepG2	liver:	n/a	n/a
2	MTA3	chr4:120220565-120222310	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:120219867-120222373	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:120221484-120222289	HepG2	liver:	n/a	n/a
5	CTCF	chr4:120222140-120222290	HFF	foreskin:	n/a	n/a
6	TAF1	chr4:120221130-120222359	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr4:120221241-120222334	HepG2	liver:	n/a	n/a
8	NFIC	chr4:120221435-120222282	HepG2	liver:	n/a	n/a
9	BHLHE40	chr4:120221906-120222330	HepG2	liver:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
10	USF1	chr4:120221606-120222270	A549	lung:	n/a	chr4:120222028-120222039 chr4:120222233-120222246 chr4:120222229-120222250
11	HDAC2	chr4:120221462-120222319	MCF-7	breast:	n/a	n/a
12	CBX3	chr4:120221000-120222352	K562	blood:	n/a	n/a
13	USF1	chr4:120221861-120222275	A549	lung:	n/a	chr4:120222028-120222039 chr4:120222233-120222246 chr4:120222229-120222250
14	MYBL2	chr4:120221364-120222368	HepG2	liver:	n/a	n/a
15	TBP	chr4:120221155-120222274	HepG2	liver:	n/a	n/a
16	NFYB	chr4:120221405-120222349	K562	blood:	n/a	chr4:120222177-120222187
17	NR2F2	chr4:120221563-120222272	MCF-7	breast:	n/a	n/a
18	USF1	chr4:120221749-120222346	H1-hESC	embryonic stem cell:	n/a	chr4:120222028-120222039 chr4:120222233-120222246 chr4:120222229-120222250
19	POLR2A	chr4:120220851-120222312	Raji	blood:	n/a	n/a
20	SP1	chr4:120221515-120222281	HepG2	liver:	n/a	chr4:120221929-120221940
21	E2F6	chr4:120221522-120222367	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr4:120221457-120222326	A549	lung:	n/a	chr4:120222234-120222245
23	HNF4A	chr4:120221494-120222303	HepG2	liver:	n/a	chr4:120221820-120221835
24	MAX	chr4:120221338-120222342	SK-N-SH	brain:	n/a	chr4:120222234-120222245
25	MAX	chr4:120221427-120222329	ECC-1	luminal epithelium:	n/a	chr4:120222234-120222245
26	MAX	chr4:120221445-120222351	MCF-7	breast:	n/a	chr4:120222234-120222245
27	BHLHE40	chr4:120221512-120222439	HepG2	liver:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
28	E2F6	chr4:120221494-120222392	H1-hESC	embryonic stem cell:	n/a	n/a
29	E2F6	chr4:120221525-120222375	A549	lung:	n/a	n/a
30	USF2	chr4:120221788-120222357	HepG2	liver:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
31	USF2	chr4:120221441-120222316	GM12878	blood:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
32	MXI1	chr4:120221537-120222282	H1-hESC	embryonic stem cell:	n/a	n/a
33	MYC	chr4:120220859-120222276	K562	blood:	n/a	chr4:120222234-120222245
34	BHLHE40	chr4:120220951-120222417	GM12878	blood:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
35	E2F6	chr4:120221481-120222324	K562	blood:	n/a	n/a
36	MYBL2	chr4:120220970-120222400	HepG2	liver:	n/a	n/a
37	NRF1	chr4:120221506-120222286	SK-N-SH	brain:	n/a	chr4:120221785-120221796 chr4:120221846-120221857
38	BHLHE40	chr4:120222000-120222352	A549	lung:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
39	MAX	chr4:120221562-120222366	MCF-7	breast:	n/a	chr4:120222234-120222245
40	MYC	chr4:120221161-120222326	NB4	blood:	n/a	chr4:120222234-120222245
41	BHLHE40	chr4:120221892-120222336	HepG2	liver:	n/a	chr4:120222233-120222246 chr4:120222229-120222250
42	MAX	chr4:120221658-120222313	HepG2	liver:	n/a	chr4:120222234-120222245
43	MBD4	chr4:120221437-120222290	HepG2	liver:	n/a	n/a
44	MAX	chr4:120221319-120222359	HepG2	liver:	n/a	chr4:120222234-120222245
45	USF1	chr4:120221804-120222358	A549	lung:	n/a	chr4:120222028-120222039 chr4:120222233-120222246 chr4:120222229-120222250
46	CREB1	chr4:120221527-120222323	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr4:120221394-120222324	A549	lung:	n/a	chr4:120222234-120222245
48	POLR2A	chr4:120221062-120222415	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr4:120221403-120222343	HL-60	blood:	n/a	n/a
50	MAZ	chr4:120220747-120222274	K562	blood:	n/a	chr4:120222234-120222245

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:120222239-120222289	HRPEpiC	eye:	n/a
2	chr4:120222222-120222272	SKMC	muscle:	n/a
3	chr4:120222239-120222289	H1-hESC	embryonic stem cell:	embryo
4	chr4:120222222-120222272	HL-60	blood:	n/a
5	chr4:120222239-120222289	HEEpiC	esophagus:	n/a
6	chr4:120222222-120222272	ProgFib	skin:	n/a
7	chr4:120222222-120222272	Hela-S3	cervix:	n/a
8	chr4:120222222-120222272	HepG2	liver:	n/a
9	chr4:120222239-120222289	CMK	blood:	n/a
10	chr4:120222239-120222289	NHBE	bronchial:	n/a
11	chr4:120222222-120222272	T-47D	breast:	n/a
12	chr4:120222222-120222272	HIPEpiC	eye:	n/a
13	chr4:120222239-120222289	BJ	skin:	n/a
14	chr4:120222239-120222289	HCM	heart:	n/a
15	chr4:120222239-120222289	GM12891	blood:	n/a
16	chr4:120222222-120222272	NT2-D1	testis:	n/a
17	chr4:120222239-120222289	HRE	kidney:	n/a
18	chr4:120222239-120222289	NB4	blood:	n/a
19	chr4:120222222-120222272	AG04450	lung:	fetal
20	chr4:120222222-120222272	MCF10A-Er-Src	breast:	n/a
21	chr4:120222239-120222289	HCPEpiC	choroid plexus:	n/a
22	chr4:120222239-120222289	SKMC	muscle:	n/a
23	chr4:120222239-120222289	GM12892	blood:	n/a
24	chr4:120222222-120222272	SK-N-MC	brain:	n/a
25	chr4:120222239-120222289	GM19239	blood:	n/a
26	chr4:120222222-120222272	AoSMC	blood vessel:	n/a
27	chr4:120222239-120222289	ProgFib	skin:	n/a
28	chr4:120222222-120222272	HUVEC	blood vessel:	n/a
29	chr4:120222222-120222272	SK-N-SH_RA	brain:	n/a
30	chr4:120222239-120222289	HIPEpiC	eye:	n/a
31	chr4:120222222-120222272	GM12878	blood:	n/a
32	chr4:120222222-120222272	AG10803	skin:	n/a
33	chr4:120222239-120222289	AG10803	skin:	n/a
34	chr4:120222222-120222272	SAEC	small airway:	n/a
35	chr4:120222239-120222289	AoSMC	blood vessel:	n/a
36	chr4:120222222-120222272	BE2_C	brain:	n/a
37	chr4:120222239-120222289	GM06990	blood:	n/a
38	chr4:120222222-120222272	HCF	heart:	n/a
39	chr4:120222239-120222289	PANC-1	pancreas:	n/a
40	chr4:120222239-120222289	HL-60	blood:	n/a
41	chr4:120222222-120222272	GM12891	blood:	n/a
42	chr4:120222239-120222289	Caco-2	colon:	n/a
43	chr4:120222239-120222289	Hepatocyte	liver:	n/a
44	chr4:120222222-120222272	HRCEpiC	kidney:	n/a
45	chr4:120222222-120222272	K562	blood:	n/a
46	chr4:120222222-120222272	GM19239	blood:	n/a
47	chr4:120222239-120222289	Jurkat	blood:	n/a
48	chr4:120222222-120222272	HCPEpiC	choroid plexus:	n/a
49	chr4:120222239-120222289	SK-N-SH	brain:	n/a
50	chr4:120222222-120222272	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr4:120132610..120134570-chr4:120221091..120222996,2	MCF-7	breast:
2	chr4:120132319..120136069-chr4:120219720..120222326,6	MCF-7	breast:
3	chr4:120132453..120136158-chr4:120220202..120223113,6	K562	blood:
4	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
5	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:
6	chr20:55840161..55841677-chr4:120221342..120223626,2	MCF-7	breast:

Variant related genes	Relation type
C4orf3	TF binding region
C4orf3	CpG island
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000164109	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17050171	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050313	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050454	1.00[AMR][1000 genomes]
rs17839113	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17839114	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17839123	1.00[AMR][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120219200-120222400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120219400-120222400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120219400-120222400	Active TSS	Fetal Intestine Large	intestine
4	chr4:120219400-120222400	Active TSS	NHLF	lung
5	chr4:120219600-120222400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr4:120219800-120222400	Active TSS	HSMM	muscle
7	chr4:120220000-120222400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:120220000-120222400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:120220000-120222400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:120220000-120222400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:120220000-120222400	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr4:120220000-120222400	Active TSS	Fetal Kidney	kidney
13	chr4:120220000-120222400	Active TSS	A549	lung
14	chr4:120220000-120222400	Active TSS	Hela-S3	cervix
15	chr4:120220000-120223200	Active TSS	GM12878-XiMat	blood
16	chr4:120220200-120222400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:120220400-120222400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr4:120220400-120222400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:120220400-120222400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:120220400-120222400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:120220400-120222400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr4:120220400-120222400	Active TSS	Fetal Intestine Small	intestine
23	chr4:120220400-120222400	Active TSS	Stomach Smooth Muscle	stomach
24	chr4:120220600-120222400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:120220600-120222400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr4:120220600-120222400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:120220600-120222400	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr4:120220600-120222400	Active TSS	Duodenum Mucosa	Duodenum
29	chr4:120220600-120222400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr4:120220600-120222400	Active TSS	Osteobl	bone
31	chr4:120220600-120222600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:120220800-120222400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr4:120220800-120222400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:120220800-120222400	Active TSS	Brain Angular Gyrus	brain
35	chr4:120220800-120222400	Active TSS	Brain Cingulate Gyrus	brain
36	chr4:120220800-120222400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr4:120220800-120222400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:120220800-120222400	Active TSS	Fetal Lung	lung
39	chr4:120220800-120222400	Active TSS	Fetal Stomach	stomach
40	chr4:120220800-120222400	Active TSS	Psoas Muscle	Psoas
41	chr4:120220800-120222400	Active TSS	Right Atrium	heart
42	chr4:120220800-120222400	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr4:120220800-120222400	Active TSS	NHEK	skin
44	chr4:120220800-120222600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:120221000-120222400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:120221000-120222400	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr4:120221000-120222400	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr4:120221000-120222400	Active TSS	Brain Anterior Caudate	brain
49	chr4:120221000-120222400	Active TSS	Brain Hippocampus Middle	brain
50	chr4:120221000-120222400	Active TSS	Brain Substantia Nigra	brain

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