Variant report

Variant	rs13138636
Chromosome Location	chr4:88312620-88312621
allele	C/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	MAZ	chr4:88312040-88312921	K562	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
2	CTCF	chr4:88312500-88312650	WI-38	lung:	n/a	n/a
3	SIN3AK20	chr4:88312139-88312797	SK-N-SH	brain:	n/a	n/a
4	TAF1	chr4:88312412-88312643	GM12878	blood:	n/a	n/a
5	MXI1	chr4:88312022-88312791	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:88311963-88312881	K562	blood:	n/a	n/a
7	MAX	chr4:88312279-88312749	MCF-7	breast:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
8	HNF4A	chr4:88311995-88312831	HepG2	liver:	n/a	chr4:88312457-88312465 chr4:88312621-88312643 chr4:88312450-88312465 chr4:88312450-88312465 chr4:88312449-88312464 chr4:88312450-88312465
9	HNF4G	chr4:88312184-88312729	HepG2	liver:	n/a	chr4:88312448-88312463 chr4:88312457-88312465 chr4:88312621-88312643 chr4:88312450-88312465 chr4:88312450-88312465 chr4:88312450-88312465
10	CTCF	chr4:88312540-88312690	GM12867	blood:	n/a	n/a
11	CTCF	chr4:88312430-88312722	Kidney_OC	kidney:	n/a	n/a
12	POLR2A	chr4:88312207-88312844	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:88312318-88312709	MCF-7	breast:	n/a	n/a
14	MAX	chr4:88312102-88312811	ECC-1	luminal epithelium:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
15	CTCF	chr4:88312600-88312750	GM12864	blood:	n/a	n/a
16	HDAC2	chr4:88312159-88312865	HepG2	liver:	n/a	n/a
17	ZNF384	chr4:88311810-88312891	GM12878	blood:	n/a	n/a
18	TAF1	chr4:88312026-88312818	K562	blood:	n/a	n/a
19	BCLAF1	chr4:88311947-88312813	GM12878	blood:	n/a	n/a
20	CTCF	chr4:88312480-88312630	HL-60	blood:	n/a	n/a
21	POLR2A	chr4:88312212-88312798	A549	lung:	n/a	n/a
22	SPI1	chr4:88312151-88312627	GM12891	blood:	n/a	n/a
23	TAF1	chr4:88312024-88312856	K562	blood:	n/a	n/a
24	BHLHE40	chr4:88311817-88312755	K562	blood:	n/a	n/a
25	GATA3	chr4:88312050-88312909	A549	lung:	n/a	chr4:88312660-88312676
26	POLR2A	chr4:88311804-88312913	HepG2	liver:	n/a	n/a
27	CTCF	chr4:88312580-88312730	GM12873	blood:	n/a	n/a
28	GTF2B	chr4:88312148-88312826	K562	blood:	n/a	n/a
29	ZNF217	chr4:88312335-88312760	MCF-7	breast:	n/a	n/a
30	CTCF	chr4:88312600-88312750	HRPEpiC	eye:	n/a	n/a
31	TCF7L2	chr4:88312194-88313063	HCT-116	colon:	n/a	n/a
32	CTCF	chr4:88312600-88312713	NHEK	skin:	n/a	n/a
33	CTCF	chr4:88312319-88312809	GM12878	blood:	n/a	n/a
34	MAZ	chr4:88312285-88312731	HepG2	liver:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
35	POLR2A	chr4:88312097-88312894	GM15510	blood:	n/a	n/a
36	MAX	chr4:88311936-88312796	Hela-S3	cervix:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
37	GABPA	chr4:88312242-88312651	MCF-7	breast:	n/a	n/a
38	CTCF	chr4:88312414-88312750	GM19238	blood:	n/a	n/a
39	MAZ	chr4:88312036-88312745	GM12878	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
40	MYC	chr4:88312322-88312859	K562	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
41	NFIC	chr4:88312081-88312779	GM12878	blood:	n/a	n/a
42	TBP	chr4:88311922-88312825	HepG2	liver:	n/a	n/a
43	ZNF143	chr4:88312202-88312747	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBP	chr4:88311667-88312786	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr4:88312255-88312668	HepG2	liver:	n/a	n/a
46	POLR2A	chr4:88311959-88312836	HepG2	liver:	n/a	n/a
47	GTF3C2	chr4:88312223-88313078	K562	blood:	n/a	n/a
48	POLR2A	chr4:88312202-88312773	GM12878	blood:	n/a	n/a
49	FOXA1	chr4:88312105-88312825	HepG2	liver:	n/a	n/a
50	CTCF	chr4:88312600-88312750	HRE	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88293477..88300868-chr4:88308814..88313684,7	K562	blood:
2	chr4:88311663..88314102-chr4:88359641..88363442,4	K562	blood:
3	chr4:88139395..88142439-chr4:88311139..88313328,4	K562	blood:
4	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:
5	chr4:88310329..88313185-chr4:88330457..88332566,2	K562	blood:
6	chr4:88294120..88296895-chr4:88310582..88312667,2	K562	blood:
7	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:

Variant related genes	Relation type
RN7SL681P	TF binding region
HSD17B11	TF binding region
ENSG00000198189	Chromatin interaction
ENSG00000145332	Chromatin interaction
ENSG00000170502	Chromatin interaction
ENSG00000249262	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10010988	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025902	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10027786	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032597	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10222732	0.82[CHB][hapmap]
rs11945232	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13103927	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13113575	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150578	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28372775	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28406846	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28502849	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28609242	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28630962	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28701008	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28736552	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34549877	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35322242	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35371368	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4314250	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6816224	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6854710	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7659182	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][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	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 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	chr4:88309000-88313200	Active TSS	Rectal Smooth Muscle	rectum
2	chr4:88309400-88312800	Active TSS	Small Intestine	intestine
3	chr4:88309400-88313000	Active TSS	NHLF	lung
4	chr4:88309600-88312800	Active TSS	Stomach Mucosa	stomach
5	chr4:88309600-88313200	Active TSS	Psoas Muscle	Psoas
6	chr4:88309600-88313200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr4:88309600-88313400	Active TSS	Stomach Smooth Muscle	stomach
8	chr4:88309800-88312800	Active TSS	Colonic Mucosa	Colon
9	chr4:88309800-88313000	Active TSS	Colon Smooth Muscle	Colon
10	chr4:88309800-88313000	Active TSS	Fetal Intestine Large	intestine
11	chr4:88309800-88313000	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr4:88309800-88313200	Active TSS	Right Atrium	heart
13	chr4:88310000-88312800	Active TSS	Fetal Intestine Small	intestine
14	chr4:88310000-88313200	Active TSS	Brain Anterior Caudate	brain
15	chr4:88310000-88313400	Active TSS	K562	blood
16	chr4:88310200-88312800	Active TSS	Hela-S3	cervix
17	chr4:88310400-88313000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:88310400-88313200	Active TSS	Left Ventricle	heart
19	chr4:88310600-88312800	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr4:88310600-88313000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr4:88310600-88313000	Active TSS	Fetal Kidney	kidney
22	chr4:88310600-88313000	Active TSS	Fetal Stomach	stomach
23	chr4:88310600-88313200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr4:88310600-88313200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:88310600-88313200	Active TSS	A549	lung
26	chr4:88310600-88313400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr4:88310800-88312800	Active TSS	Fetal Brain Female	brain
28	chr4:88310800-88313000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:88310800-88313000	Active TSS	Brain Germinal Matrix	brain
30	chr4:88310800-88313000	Active TSS	Esophagus	oesophagus
31	chr4:88310800-88313000	Active TSS	Lung	lung
32	chr4:88310800-88313200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:88310800-88313200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:88310800-88313200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:88310800-88313200	Active TSS	Brain Angular Gyrus	brain
36	chr4:88310800-88313200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:88310800-88313200	Active TSS	Brain Substantia Nigra	brain
38	chr4:88310800-88313200	Active TSS	Ovary	ovary
39	chr4:88310800-88313200	Active TSS	Right Ventricle	heart
40	chr4:88311000-88312800	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr4:88311000-88312800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr4:88311000-88312800	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr4:88311000-88312800	Active TSS	NHDF-Ad	bronchial
44	chr4:88311000-88313000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:88311000-88313000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr4:88311000-88313000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr4:88311000-88313000	Active TSS	Muscle Satellite Cultured Cells	--
48	chr4:88311000-88313000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr4:88311000-88313200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:88311000-88313200	Active TSS	Duodenum Mucosa	Duodenum

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