Variant report

Variant	rs13138404
Chromosome Location	chr4:88312504-88312505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:475)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:475 , 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	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	chr4:88312430-88312722	Kidney_OC	kidney:	n/a	n/a
11	POLR2A	chr4:88312207-88312844	HepG2	liver:	n/a	n/a
12	POLR2A	chr4:88312318-88312709	MCF-7	breast:	n/a	n/a
13	MAX	chr4:88312102-88312811	ECC-1	luminal epithelium:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
14	HDAC2	chr4:88312159-88312865	HepG2	liver:	n/a	n/a
15	ZNF384	chr4:88311810-88312891	GM12878	blood:	n/a	n/a
16	TAF1	chr4:88312026-88312818	K562	blood:	n/a	n/a
17	BCLAF1	chr4:88311947-88312813	GM12878	blood:	n/a	n/a
18	CTCF	chr4:88312480-88312630	HL-60	blood:	n/a	n/a
19	POLR2A	chr4:88312212-88312798	A549	lung:	n/a	n/a
20	CTCF	chr4:88312400-88312550	GM12878	blood:	n/a	n/a
21	SPI1	chr4:88312151-88312627	GM12891	blood:	n/a	n/a
22	CTCF	chr4:88312400-88312550	WERI-Rb-1	eye:	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	chr4:88312440-88312590	HUVEC	blood vessel:	n/a	n/a
28	GTF2B	chr4:88312148-88312826	K562	blood:	n/a	n/a
29	POLR2A	chr4:88312278-88312617	MCF-7	breast:	n/a	n/a
30	ZNF217	chr4:88312335-88312760	MCF-7	breast:	n/a	n/a
31	CTCF	chr4:88312420-88312570	HepG2	liver:	n/a	n/a
32	TCF7L2	chr4:88312194-88313063	HCT-116	colon:	n/a	n/a
33	CEBPB	chr4:88312290-88312585	HepG2	liver:	n/a	n/a
34	CTCF	chr4:88312319-88312809	GM12878	blood:	n/a	n/a
35	MAZ	chr4:88312285-88312731	HepG2	liver:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
36	POLR2A	chr4:88312097-88312894	GM15510	blood:	n/a	n/a
37	MAX	chr4:88311936-88312796	Hela-S3	cervix:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
38	GABPA	chr4:88312242-88312651	MCF-7	breast:	n/a	n/a
39	CTCF	chr4:88312414-88312750	GM19238	blood:	n/a	n/a
40	MAZ	chr4:88312036-88312745	GM12878	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
41	MYC	chr4:88312322-88312859	K562	blood:	n/a	chr4:88312504-88312511 chr4:88312500-88312509
42	NFIC	chr4:88312081-88312779	GM12878	blood:	n/a	n/a
43	TBP	chr4:88311922-88312825	HepG2	liver:	n/a	n/a
44	ZNF143	chr4:88312202-88312747	H1-hESC	embryonic stem cell:	n/a	n/a
45	TBP	chr4:88311667-88312786	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr4:88312460-88312610	WERI-Rb-1	eye:	n/a	n/a
47	RAD21	chr4:88312255-88312668	HepG2	liver:	n/a	n/a
48	FOS	chr4:88312415-88312556	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr4:88311959-88312836	HepG2	liver:	n/a	n/a
50	GTF3C2	chr4:88312223-88313078	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:88312455-88312505	NH-A	brain:	n/a
2	chr4:88312455-88312505	MCF10A-Er-Src	breast:	n/a
3	chr4:88312455-88312505	NHDF-neo	bronchial:	n/a
4	chr4:88312455-88312505	HUVEC	blood vessel:	n/a
5	chr4:88312455-88312505	SAEC	small airway:	n/a
6	chr4:88312455-88312505	NT2-D1	testis:	n/a
7	chr4:88312455-88312505	MCF-7	breast:	n/a
8	chr4:88312455-88312505	HCF	heart:	n/a
9	chr4:88312455-88312505	HAEpiC	amniotic membrane:	n/a
10	chr4:88312455-88312505	AG04450	lung:	fetal
11	chr4:88312455-88312505	K562	blood:	n/a
12	chr4:88312455-88312505	PrEC	prostate:	n/a
13	chr4:88312455-88312505	H1-hESC	embryonic stem cell:	embryo
14	chr4:88312455-88312505	ProgFib	skin:	n/a
15	chr4:88312455-88312505	AG09319	gingival:	n/a
16	chr4:88312455-88312505	HCM	heart:	n/a
17	chr4:88312455-88312505	BJ	skin:	n/a
18	chr4:88312455-88312505	AoSMC	blood vessel:	n/a
19	chr4:88312455-88312505	HepG2	liver:	n/a
20	chr4:88312455-88312505	HMEC	breast:	n/a
21	chr4:88312455-88312505	ovcar-3	ovarian:	n/a
22	chr4:88312455-88312505	GM06990	blood:	n/a
23	chr4:88312455-88312505	U87	brain:	n/a
24	chr4:88312455-88312505	Caco-2	colon:	n/a
25	chr4:88312455-88312505	HEEpiC	esophagus:	n/a
26	chr4:88312455-88312505	T-47D	breast:	n/a
27	chr4:88312455-88312505	HL-60	blood:	n/a
28	chr4:88312455-88312505	HCPEpiC	choroid plexus:	n/a
29	chr4:88312455-88312505	HIPEpiC	eye:	n/a
30	chr4:88312455-88312505	HRE	kidney:	n/a
31	chr4:88312455-88312505	AG10803	skin:	n/a
32	chr4:88312455-88312505	HPAEpiC	pulmonary alveolar:	n/a
33	chr4:88312455-88312505	AG09309	skin:	n/a
34	chr4:88312455-88312505	LNCaP	prostate:	n/a
35	chr4:88312455-88312505	Hela-S3	cervix:	n/a
36	chr4:88312455-88312505	HEK293	kidney:	embryo
37	chr4:88312455-88312505	CMK	blood:	n/a
38	chr4:88312455-88312505	RPTEC	kidney:	n/a
39	chr4:88312455-88312505	HRPEpiC	eye:	n/a
40	chr4:88312455-88312505	SK-N-SH_RA	brain:	n/a
41	chr4:88312455-88312505	PFSK-1	brain:	n/a
42	chr4:88312455-88312505	PANC-1	pancreas:	n/a
43	chr4:88312455-88312505	HNPCEpiC	eye:	n/a
44	chr4:88312455-88312505	A549	lung:	n/a
45	chr4:88312455-88312505	GM12892	blood:	n/a
46	chr4:88312455-88312505	HRCEpiC	kidney:	n/a
47	chr4:88312455-88312505	AG04449	skin:	fetal
48	chr4:88312455-88312505	IMR90	lung:	fetal
49	chr4:88312455-88312505	GM12891	blood:	n/a
50	chr4:88312455-88312505	GM12878	blood:	n/a

(count:7 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10010988	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10025902	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10027786	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10032597	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10222732	0.82[CHB][hapmap]
rs11945232	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13103927	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13113575	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13138636	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	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28372775	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28406846	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28502849	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28609242	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28630962	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28701008	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28736552	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34549877	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35322242	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35371368	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4314250	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816224	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6854710	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7659182	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13138404	HSD17B13	cis	parietal	SCAN

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	chr4:88310000-88312600	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr4:88310000-88312800	Active TSS	Fetal Intestine Small	intestine
15	chr4:88310000-88313200	Active TSS	Brain Anterior Caudate	brain
16	chr4:88310000-88313400	Active TSS	K562	blood
17	chr4:88310200-88312800	Active TSS	Hela-S3	cervix
18	chr4:88310400-88313000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:88310400-88313200	Active TSS	Left Ventricle	heart
20	chr4:88310600-88312800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr4:88310600-88313000	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr4:88310600-88313000	Active TSS	Fetal Kidney	kidney
23	chr4:88310600-88313000	Active TSS	Fetal Stomach	stomach
24	chr4:88310600-88313200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr4:88310600-88313200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:88310600-88313200	Active TSS	A549	lung
27	chr4:88310600-88313400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr4:88310800-88312600	Active TSS	Pancreas	Pancrea
29	chr4:88310800-88312800	Active TSS	Fetal Brain Female	brain
30	chr4:88310800-88313000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:88310800-88313000	Active TSS	Brain Germinal Matrix	brain
32	chr4:88310800-88313000	Active TSS	Esophagus	oesophagus
33	chr4:88310800-88313000	Active TSS	Lung	lung
34	chr4:88310800-88313200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:88310800-88313200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:88310800-88313200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:88310800-88313200	Active TSS	Brain Angular Gyrus	brain
38	chr4:88310800-88313200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:88310800-88313200	Active TSS	Brain Substantia Nigra	brain
40	chr4:88310800-88313200	Active TSS	Ovary	ovary
41	chr4:88310800-88313200	Active TSS	Right Ventricle	heart
42	chr4:88311000-88312600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:88311000-88312800	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr4:88311000-88312800	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr4:88311000-88312800	Active TSS	Monocytes-CD14+_RO01746	blood
46	chr4:88311000-88312800	Active TSS	NHDF-Ad	bronchial
47	chr4:88311000-88313000	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr4:88311000-88313000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr4:88311000-88313000	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr4:88311000-88313000	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links