Variant report

Variant	rs35571699
Chromosome Location	chr4:106395144-106395145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:479)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:479 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr4:106394970-106395361	GM12878	blood:	n/a	n/a
2	YY1	chr4:106394480-106395403	K562	blood:	n/a	n/a
3	SRF	chr4:106395065-106395331	K562	blood:	n/a	n/a
4	POLR2A	chr4:106394631-106395366	HepG2	liver:	n/a	n/a
5	ATF3	chr4:106395029-106395347	K562	blood:	n/a	n/a
6	POLR2A	chr4:106394156-106395552	MCF-7	breast:	n/a	n/a
7	THAP1	chr4:106395117-106395313	K562	blood:	n/a	n/a
8	ATF2	chr4:106394994-106395501	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr4:106393774-106395787	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr4:106395103-106395384	SK-N-SH_RA	brain:	n/a	chr4:106395270-106395288 chr4:106395271-106395287
11	CTCF	chr4:106395085-106395459	K562	blood:	n/a	chr4:106395270-106395288 chr4:106395271-106395287
12	POLR2A	chr4:106394126-106395409	Hela-S3	cervix:	n/a	n/a
13	BRCA1	chr4:106394554-106395335	Hela-S3	cervix:	n/a	n/a
14	WRNIP1	chr4:106395096-106395560	GM12878	blood:	n/a	n/a
15	MAX	chr4:106395026-106395412	A549	lung:	n/a	n/a
16	RUNX3	chr4:106394071-106395523	GM12878	blood:	n/a	n/a
17	E2F4	chr4:106394509-106395522	MCF10A-Er-Src	breast:	n/a	chr4:106395296-106395308
18	ELF1	chr4:106394112-106395480	GM12878	blood:	n/a	chr4:106395298-106395310
19	GTF2F1	chr4:106395100-106395518	Hela-S3	cervix:	n/a	n/a
20	YY1	chr4:106395056-106395318	A549	lung:	n/a	n/a
21	HEY1	chr4:106394464-106395302	HepG2	liver:	n/a	n/a
22	SMC3	chr4:106394196-106395510	Hela-S3	cervix:	n/a	chr4:106395272-106395286
23	TEAD4	chr4:106395022-106395563	H1-hESC	embryonic stem cell:	n/a	n/a
24	IRF4	chr4:106394983-106395495	GM12878	blood:	n/a	n/a
25	CTCF	chr4:106395131-106395427	GM20000	blood:	n/a	chr4:106395270-106395288 chr4:106395271-106395287
26	TAF1	chr4:106394996-106395345	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr4:106394961-106395330	GM12878	blood:	n/a	n/a
28	CREB1	chr4:106394936-106395509	K562	blood:	n/a	n/a
29	CTCF	chr4:106395088-106395452	GM12892	blood:	n/a	chr4:106395270-106395288 chr4:106395271-106395287
30	JUND	chr4:106394955-106395475	A549	lung:	n/a	n/a
31	POLR2A	chr4:106394323-106395483	PFSK-1	brain:	n/a	n/a
32	STAT5A	chr4:106393948-106395519	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:106394140-106395476	GM15510	blood:	n/a	n/a
34	POLR2A	chr4:106394186-106395377	Hela-S3	cervix:	n/a	n/a
35	MXI1	chr4:106394186-106395625	HepG2	liver:	n/a	n/a
36	CEBPB	chr4:106394941-106395537	GM12878	blood:	n/a	n/a
37	RAD21	chr4:106395129-106395421	SK-N-SH_RA	brain:	n/a	chr4:106395243-106395252 chr4:106395268-106395287 chr4:106395270-106395282
38	RCOR1	chr4:106394382-106395452	HepG2	liver:	n/a	n/a
39	POLR2A	chr4:106394955-106395328	A549	lung:	n/a	n/a
40	RAD21	chr4:106395064-106395459	HepG2	liver:	n/a	chr4:106395243-106395252 chr4:106395268-106395287 chr4:106395270-106395282
41	CTCF	chr4:106395108-106395446	GM19240	blood:	n/a	chr4:106395270-106395288 chr4:106395271-106395287
42	CREB1	chr4:106394896-106395367	A549	lung:	n/a	n/a
43	POLR2A	chr4:106394218-106395478	HUVEC	blood vessel:	n/a	n/a
44	MYC	chr4:106394684-106395520	H1-hESC	embryonic stem cell:	n/a	n/a
45	RELA	chr4:106394120-106395420	GM12891	blood:	n/a	n/a
46	TAF1	chr4:106394422-106395460	ECC-1	luminal epithelium:	n/a	n/a
47	POU2F2	chr4:106394968-106395349	GM12878	blood:	n/a	n/a
48	GATA3	chr4:106395117-106395369	T-47D	breast:	n/a	n/a
49	MAX	chr4:106394196-106395554	HepG2	liver:	n/a	chr4:106394329-106394338
50	CBX3	chr4:106394936-106395545	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:106395119-106395169	ProgFib	skin:	n/a
2	chr4:106395119-106395169	HCPEpiC	choroid plexus:	n/a
3	chr4:106395119-106395169	HRE	kidney:	n/a
4	chr4:106395119-106395169	T-47D	breast:	n/a
5	chr4:106395119-106395169	RPTEC	kidney:	n/a
6	chr4:106395119-106395169	SK-N-MC	brain:	n/a
7	chr4:106395119-106395169	HEEpiC	esophagus:	n/a
8	chr4:106395119-106395169	U87	brain:	n/a
9	chr4:106395119-106395169	IMR90	lung:	fetal
10	chr4:106395119-106395169	NT2-D1	testis:	n/a
11	chr4:106395119-106395169	SK-N-SH	brain:	n/a
12	chr4:106395119-106395169	HRPEpiC	eye:	n/a
13	chr4:106395119-106395169	HPAEpiC	pulmonary alveolar:	n/a
14	chr4:106395119-106395169	HIPEpiC	eye:	n/a
15	chr4:106395119-106395169	HMEC	breast:	n/a
16	chr4:106395119-106395169	ECC-1	luminal epithelium:	n/a
17	chr4:106395119-106395169	PrEC	prostate:	n/a
18	chr4:106395119-106395169	MCF-7	breast:	n/a
19	chr4:106395119-106395169	GM12878	blood:	n/a
20	chr4:106395119-106395169	NH-A	brain:	n/a
21	chr4:106395119-106395169	HAEpiC	amniotic membrane:	n/a
22	chr4:106395119-106395169	HL-60	blood:	n/a
23	chr4:106395119-106395169	SKMC	muscle:	n/a
24	chr4:106395119-106395169	AG04449	skin:	fetal
25	chr4:106395119-106395169	CMK	blood:	n/a
26	chr4:106395119-106395169	Hepatocyte	liver:	n/a
27	chr4:106395119-106395169	HNPCEpiC	eye:	n/a
28	chr4:106395119-106395169	BJ	skin:	n/a
29	chr4:106395119-106395169	HCM	heart:	n/a
30	chr4:106395119-106395169	H1-hESC	embryonic stem cell:	embryo
31	chr4:106395119-106395169	AG09309	skin:	n/a
32	chr4:106395119-106395169	HCT-116	colon:	n/a
33	chr4:106395119-106395169	SK-N-SH_RA	brain:	n/a
34	chr4:106395119-106395169	MCF10A-Er-Src	breast:	n/a
35	chr4:106395119-106395169	SAEC	small airway:	n/a
36	chr4:106395119-106395169	GM06990	blood:	n/a
37	chr4:106395119-106395169	Jurkat	blood:	n/a
38	chr4:106395119-106395169	NB4	blood:	n/a
39	chr4:106395119-106395169	PFSK-1	brain:	n/a
40	chr4:106395119-106395169	Hela-S3	cervix:	n/a
41	chr4:106395119-106395169	AG10803	skin:	n/a
42	chr4:106395119-106395169	HEK293	kidney:	embryo
43	chr4:106395119-106395169	A549	lung:	n/a
44	chr4:106395119-106395169	PANC-1	pancreas:	n/a
45	chr4:106395119-106395169	Caco-2	colon:	n/a
46	chr4:106395119-106395169	BE2_C	brain:	n/a
47	chr4:106395119-106395169	HepG2	liver:	n/a
48	chr4:106395119-106395169	ovcar-3	ovarian:	n/a
49	chr4:106395119-106395169	LNCaP	prostate:	n/a
50	chr4:106395119-106395169	AG04450	lung:	fetal

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106394755..106397717-chr4:106629970..106632343,2	MCF-7	breast:
2	chr4:106393178..106395974-chr4:106403458..106406397,4	K562	blood:
3	chr4:106319989..106322033-chr4:106394167..106395857,2	K562	blood:
4	chr4:106066586..106070319-chr4:106392729..106397085,7	MCF-7	breast:
5	chr4:106393672..106395391-chr4:106404396..106406000,2	MCF-7	breast:
6	chr4:106393678..106396634-chr4:106628055..106631625,3	K562	blood:
7	chr19:39340223..39340777-chr4:106394690..106395372,2	NB4	blood:
8	chr4:105893495..105895146-chr4:106393920..106395691,2	MCF-7	breast:
9	chr4:106393662..106395828-chr4:106816451..106818779,3	MCF-7	breast:
10	chr4:106066539..106069010-chr4:106392150..106395317,5	MCF-7	breast:
11	chr4:106393199..106396342-chr4:106628328..106631625,4	K562	blood:
12	chr4:106066580..106068131-chr4:106393738..106396130,2	K562	blood:
13	chr1:149223985..149224640-chr4:106394223..106395221,2	Hela-S3	cervix:
14	chr17:56735181..56736729-chr4:106394979..106396822,2	MCF-7	breast:
15	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:
16	chr4:106394828..106395492-chr4:106629382..106630203,2	K562	blood:
17	chr4:106368037..106370559-chr4:106393297..106395424,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPA2	TF binding region
PPA2	CpG island
ENSG00000248373	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000168769	Chromatin interaction
ENSG00000138780	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000249264	Chromatin interaction
ENSG00000168743	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10516518	0.83[EUR][1000 genomes]
rs11097888	0.90[EUR][1000 genomes]
rs12108622	0.90[EUR][1000 genomes]
rs17035601	0.90[EUR][1000 genomes]
rs17035603	0.90[EUR][1000 genomes]
rs17035607	0.90[EUR][1000 genomes]
rs17035612	0.90[EUR][1000 genomes]
rs17035614	0.90[EUR][1000 genomes]
rs17035625	0.90[EUR][1000 genomes]
rs28415199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56042714	0.90[EUR][1000 genomes]
rs59758094	0.90[EUR][1000 genomes]
rs60063074	0.90[EUR][1000 genomes]
rs72950599	0.90[EUR][1000 genomes]
rs72952282	0.90[EUR][1000 genomes]
rs72952292	0.90[EUR][1000 genomes]
rs72952299	0.90[EUR][1000 genomes]
rs72954316	0.90[EUR][1000 genomes]
rs73836215	0.90[EUR][1000 genomes]
rs73836216	0.90[EUR][1000 genomes]
rs73836268	0.90[EUR][1000 genomes]
rs73836269	0.90[EUR][1000 genomes]
rs73836273	0.90[EUR][1000 genomes]
rs73836279	0.90[EUR][1000 genomes]
rs7671891	0.90[EUR][1000 genomes]
rs9685855	0.90[EUR][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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv3421073	chr4:106393528-106396476	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 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	chr4:106392800-106395600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:106393000-106395400	Active TSS	Fetal Muscle Trunk	muscle
3	chr4:106393000-106395400	Active TSS	Right Atrium	heart
4	chr4:106393000-106395600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:106393400-106395400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106393400-106395400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:106393400-106395400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:106393400-106395400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:106393400-106395600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:106393400-106395600	Active TSS	Right Ventricle	heart
11	chr4:106393600-106395400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:106393600-106395400	Active TSS	Left Ventricle	heart
13	chr4:106393600-106395400	Active TSS	Stomach Mucosa	stomach
14	chr4:106393600-106395600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:106393600-106395600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:106393600-106395600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr4:106393600-106395600	Active TSS	Colon Smooth Muscle	Colon
18	chr4:106393600-106395600	Active TSS	Fetal Stomach	stomach
19	chr4:106393600-106395600	Active TSS	A549	lung
20	chr4:106393600-106395600	Active TSS	GM12878-XiMat	blood
21	chr4:106393600-106395800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:106393600-106395800	Active TSS	HMEC	breast
23	chr4:106393600-106395800	Active TSS	K562	blood
24	chr4:106393800-106395200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:106393800-106395400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr4:106393800-106395400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr4:106393800-106395400	Active TSS	Fetal Intestine Small	intestine
28	chr4:106393800-106395400	Active TSS	HepG2	liver
29	chr4:106393800-106395600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:106393800-106395600	Active TSS	Colonic Mucosa	Colon
31	chr4:106393800-106395600	Active TSS	Thymus	Thymus
32	chr4:106393800-106395600	Active TSS	HSMM	muscle
33	chr4:106393800-106395600	Active TSS	HSMMtube	muscle
34	chr4:106394000-106395200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:106394000-106395200	Active TSS	Esophagus	oesophagus
36	chr4:106394000-106395200	Active TSS	Lung	lung
37	chr4:106394000-106395200	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr4:106394000-106395400	Active TSS	H1 Cell Line	embryonic stem cell
39	chr4:106394000-106395400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:106394000-106395400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:106394000-106395400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:106394000-106395400	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr4:106394000-106395400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:106394000-106395400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:106394000-106395400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:106394000-106395400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr4:106394000-106395400	Active TSS	Brain Angular Gyrus	brain
48	chr4:106394000-106395400	Active TSS	Brain Hippocampus Middle	brain
49	chr4:106394000-106395400	Active TSS	Fetal Intestine Large	intestine
50	chr4:106394000-106395400	Active TSS	Gastric	stomach

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