Variant report

Variant	rs28654511
Chromosome Location	chr4:88312293-88312294
allele	A/T
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	SIN3AK20	chr4:88312139-88312797	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr4:88312022-88312791	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:88311963-88312881	K562	blood:	n/a	n/a
5	MAX	chr4:88312279-88312749	MCF-7	breast:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
6	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
7	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
8	POLR2A	chr4:88312207-88312844	HepG2	liver:	n/a	n/a
9	MAX	chr4:88312102-88312811	ECC-1	luminal epithelium:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
10	HDAC2	chr4:88312159-88312865	HepG2	liver:	n/a	n/a
11	ZNF384	chr4:88311810-88312891	GM12878	blood:	n/a	n/a
12	TAF1	chr4:88312026-88312818	K562	blood:	n/a	n/a
13	BCLAF1	chr4:88311947-88312813	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:88312212-88312798	A549	lung:	n/a	n/a
15	SPI1	chr4:88312151-88312627	GM12891	blood:	n/a	n/a
16	TAF1	chr4:88312024-88312856	K562	blood:	n/a	n/a
17	BHLHE40	chr4:88311817-88312755	K562	blood:	n/a	n/a
18	GATA3	chr4:88312050-88312909	A549	lung:	n/a	chr4:88312660-88312676
19	POLR2A	chr4:88311804-88312913	HepG2	liver:	n/a	n/a
20	GTF2B	chr4:88312148-88312826	K562	blood:	n/a	n/a
21	POLR2A	chr4:88312278-88312617	MCF-7	breast:	n/a	n/a
22	TCF7L2	chr4:88312194-88313063	HCT-116	colon:	n/a	n/a
23	CEBPB	chr4:88312290-88312585	HepG2	liver:	n/a	n/a
24	MAZ	chr4:88312285-88312731	HepG2	liver:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
25	POLR2A	chr4:88312097-88312894	GM15510	blood:	n/a	n/a
26	MAX	chr4:88311936-88312796	Hela-S3	cervix:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
27	GABPA	chr4:88312242-88312651	MCF-7	breast:	n/a	n/a
28	MAZ	chr4:88312036-88312745	GM12878	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
29	GABPA	chr4:88312265-88312432	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr4:88312081-88312779	GM12878	blood:	n/a	n/a
31	TBP	chr4:88311922-88312825	HepG2	liver:	n/a	n/a
32	ZNF143	chr4:88312202-88312747	H1-hESC	embryonic stem cell:	n/a	n/a
33	TBP	chr4:88311667-88312786	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr4:88312255-88312668	HepG2	liver:	n/a	n/a
35	POLR2A	chr4:88311959-88312836	HepG2	liver:	n/a	n/a
36	GTF3C2	chr4:88312223-88313078	K562	blood:	n/a	n/a
37	POLR2A	chr4:88312202-88312773	GM12878	blood:	n/a	n/a
38	FOXA1	chr4:88312105-88312825	HepG2	liver:	n/a	n/a
39	EP300	chr4:88312162-88312642	Hela-S3	cervix:	n/a	n/a
40	ELF1	chr4:88312269-88312780	GM12878	blood:	n/a	n/a
41	MYC	chr4:88311762-88312796	K562	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509 chr4:88311838-88311851
42	CEBPB	chr4:88312198-88312700	A549	lung:	n/a	n/a
43	POLR2A	chr4:88312029-88312818	U87	brain:	n/a	n/a
44	TRIM28	chr4:88311861-88312862	K562	blood:	n/a	n/a
45	CEBPB	chr4:88312121-88312650	HepG2	liver:	n/a	n/a
46	CUX1	chr4:88311601-88312799	K562	blood:	n/a	chr4:88311726-88311735
47	CEBPB	chr4:88311911-88312850	K562	blood:	n/a	n/a
48	TBL1XR1	chr4:88312051-88312909	K562	blood:	n/a	n/a
49	HDAC2	chr4:88312135-88312792	HepG2	liver:	n/a	n/a
50	FOXM1	chr4:88312005-88312801	ECC-1	luminal epithelium:	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
ENSG00000170502	Chromatin interaction
ENSG00000249262	Chromatin interaction
ENSG00000198189	Chromatin interaction
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28713542	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34856449	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826695	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6827817	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7688038	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7699237	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	chr4:88309000-88312400	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr4:88309000-88313200	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:88309400-88312800	Active TSS	Small Intestine	intestine
4	chr4:88309400-88313000	Active TSS	NHLF	lung
5	chr4:88309600-88312800	Active TSS	Stomach Mucosa	stomach
6	chr4:88309600-88313200	Active TSS	Psoas Muscle	Psoas
7	chr4:88309600-88313200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr4:88309600-88313400	Active TSS	Stomach Smooth Muscle	stomach
9	chr4:88309800-88312800	Active TSS	Colonic Mucosa	Colon
10	chr4:88309800-88313000	Active TSS	Colon Smooth Muscle	Colon
11	chr4:88309800-88313000	Active TSS	Fetal Intestine Large	intestine
12	chr4:88309800-88313000	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr4:88309800-88313200	Active TSS	Right Atrium	heart
14	chr4:88310000-88312600	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:88310000-88312800	Active TSS	Fetal Intestine Small	intestine
16	chr4:88310000-88313200	Active TSS	Brain Anterior Caudate	brain
17	chr4:88310000-88313400	Active TSS	K562	blood
18	chr4:88310200-88312800	Active TSS	Hela-S3	cervix
19	chr4:88310400-88313000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:88310400-88313200	Active TSS	Left Ventricle	heart
21	chr4:88310600-88312800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:88310600-88313000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:88310600-88313000	Active TSS	Fetal Kidney	kidney
24	chr4:88310600-88313000	Active TSS	Fetal Stomach	stomach
25	chr4:88310600-88313200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:88310600-88313200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:88310600-88313200	Active TSS	A549	lung
28	chr4:88310600-88313400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr4:88310800-88312600	Active TSS	Pancreas	Pancrea
30	chr4:88310800-88312800	Active TSS	Fetal Brain Female	brain
31	chr4:88310800-88313000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:88310800-88313000	Active TSS	Brain Germinal Matrix	brain
33	chr4:88310800-88313000	Active TSS	Esophagus	oesophagus
34	chr4:88310800-88313000	Active TSS	Lung	lung
35	chr4:88310800-88313200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:88310800-88313200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:88310800-88313200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:88310800-88313200	Active TSS	Brain Angular Gyrus	brain
39	chr4:88310800-88313200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:88310800-88313200	Active TSS	Brain Substantia Nigra	brain
41	chr4:88310800-88313200	Active TSS	Ovary	ovary
42	chr4:88310800-88313200	Active TSS	Right Ventricle	heart
43	chr4:88311000-88312600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:88311000-88312800	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr4:88311000-88312800	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr4:88311000-88312800	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr4:88311000-88312800	Active TSS	NHDF-Ad	bronchial
48	chr4:88311000-88313000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr4:88311000-88313000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr4:88311000-88313000	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links