Variant report

Variant	rs4314250
Chromosome Location	chr4:88340969-88340970
allele	C/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	REST	chr4:88340471-88341155	PFSK-1	brain:	n/a	n/a
2	CEBPB	chr4:88340564-88341098	MCF-7	breast:	n/a	n/a
3	GATA3	chr4:88340631-88341203	MCF-7	breast:	n/a	n/a
4	HNF4G	chr4:88340691-88341223	HepG2	liver:	n/a	chr4:88341011-88341025 chr4:88341011-88341026 chr4:88341011-88341024 chr4:88340932-88340947 chr4:88340932-88340947 chr4:88341012-88341025 chr4:88341011-88341026 chr4:88341012-88341024
5	RCOR1	chr4:88340917-88341251	K562	blood:	n/a	n/a
6	FOXA1	chr4:88340600-88340996	T-47D	breast:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
7	FOXM1	chr4:88340613-88341268	MCF-7	breast:	n/a	n/a
8	MYBL2	chr4:88340548-88341440	HepG2	liver:	n/a	n/a
9	MBD4	chr4:88340538-88341166	HepG2	liver:	n/a	n/a
10	USF1	chr4:88340657-88341082	A549	lung:	n/a	n/a
11	MXI1	chr4:88340590-88341227	HepG2	liver:	n/a	n/a
12	FOXA1	chr4:88340521-88341390	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
13	HDAC2	chr4:88340524-88341333	MCF-7	breast:	n/a	chr4:88341238-88341252
14	FOSL2	chr4:88340483-88341322	A549	lung:	n/a	chr4:88340917-88340927 chr4:88340915-88340926
15	MAFF	chr4:88340669-88341137	HepG2	liver:	n/a	n/a
16	NR3C1	chr4:88340593-88341048	A549	lung:	n/a	n/a
17	HNF4A	chr4:88340571-88341197	HepG2	liver:	n/a	chr4:88341011-88341025 chr4:88341011-88341026 chr4:88341011-88341024 chr4:88340932-88340947 chr4:88340932-88340947 chr4:88341012-88341025 chr4:88341011-88341026 chr4:88341012-88341024
18	GATA3	chr4:88340315-88341503	MCF-7	breast:	n/a	n/a
19	MAFK	chr4:88340339-88341278	HepG2	liver:	n/a	n/a
20	TCF7L2	chr4:88340660-88341212	MCF-7	breast:	n/a	n/a
21	NR3C1	chr4:88340560-88340988	A549	lung:	n/a	n/a
22	JUN	chr4:88340692-88341074	HepG2	liver:	n/a	chr4:88340917-88340927
23	SP1	chr4:88340472-88341391	A549	lung:	n/a	n/a
24	TCF12	chr4:88340415-88341417	MCF-7	breast:	n/a	chr4:88340755-88340764
25	SP1	chr4:88340541-88341287	HepG2	liver:	n/a	n/a
26	ZNF217	chr4:88340378-88341204	MCF-7	breast:	n/a	n/a
27	HDAC2	chr4:88340489-88341209	HepG2	liver:	n/a	n/a
28	TCF12	chr4:88340583-88341050	A549	lung:	n/a	chr4:88340755-88340764
29	HDAC2	chr4:88340471-88341258	HepG2	liver:	n/a	chr4:88341238-88341252
30	EP300	chr4:88340390-88341191	A549	lung:	n/a	chr4:88340877-88340887
31	NR2F2	chr4:88340631-88341292	MCF-7	breast:	n/a	n/a
32	RXRA	chr4:88340632-88341119	HepG2	liver:	n/a	n/a
33	MYBL2	chr4:88340505-88341446	HepG2	liver:	n/a	n/a
34	FOXA1	chr4:88340477-88341336	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
35	MAX	chr4:88340585-88341174	MCF-7	breast:	n/a	n/a
36	SP1	chr4:88340515-88341191	A549	lung:	n/a	n/a
37	JUND	chr4:88340611-88341176	A549	lung:	n/a	chr4:88340917-88340927 chr4:88340916-88340927
38	GATA3	chr4:88340654-88341167	MCF-7	breast:	n/a	n/a
39	NR3C1	chr4:88340576-88341161	A549	lung:	n/a	n/a
40	FOXA1	chr4:88340501-88341381	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
41	NR2F2	chr4:88340664-88341294	HepG2	liver:	n/a	n/a
42	HDAC2	chr4:88340509-88341225	MCF-7	breast:	n/a	n/a
43	EP300	chr4:88340598-88341223	HepG2	liver:	n/a	chr4:88340877-88340887
44	JUND	chr4:88340703-88341173	HepG2	liver:	n/a	chr4:88340917-88340927 chr4:88340916-88340927
45	TCF12	chr4:88340585-88341047	HepG2	liver:	n/a	chr4:88340755-88340764
46	EP300	chr4:88340471-88341109	A549	lung:	n/a	chr4:88340877-88340887
47	FOSL2	chr4:88340509-88341180	MCF-7	breast:	n/a	chr4:88340917-88340927 chr4:88340915-88340926
48	FOSL2	chr4:88340733-88340969	A549	lung:	n/a	chr4:88340917-88340927 chr4:88340915-88340926
49	GATA2	chr4:88340751-88341286	HUVEC	blood vessel:	n/a	n/a
50	SMC3	chr4:88340697-88341330	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:88340947-88340997	HCM	heart:	n/a
2	chr4:88340947-88340997	NHDF-neo	bronchial:	n/a
3	chr4:88340947-88340997	SKMC	muscle:	n/a
4	chr4:88340947-88340997	SK-N-MC	brain:	n/a
5	chr4:88340947-88340997	NB4	blood:	n/a
6	chr4:88340947-88340997	HepG2	liver:	n/a
7	chr4:88340947-88340997	IMR90	lung:	fetal
8	chr4:88340947-88340997	HUVEC	blood vessel:	n/a
9	chr4:88340947-88340997	RPTEC	kidney:	n/a
10	chr4:88340947-88340997	MCF-7	breast:	n/a
11	chr4:88340947-88340997	ECC-1	luminal epithelium:	n/a
12	chr4:88340947-88340997	BE2_C	brain:	n/a
13	chr4:88340947-88340997	AG04450	lung:	fetal
14	chr4:88340947-88340997	HL-60	blood:	n/a
15	chr4:88340947-88340997	Caco-2	colon:	n/a
16	chr4:88340947-88340997	K562	blood:	n/a
17	chr4:88340947-88340997	MCF10A-Er-Src	breast:	n/a
18	chr4:88340947-88340997	GM06990	blood:	n/a
19	chr4:88340947-88340997	AG10803	skin:	n/a
20	chr4:88340947-88340997	AoSMC	blood vessel:	n/a
21	chr4:88340947-88340997	ovcar-3	ovarian:	n/a
22	chr4:88340947-88340997	Hela-S3	cervix:	n/a
23	chr4:88340947-88340997	HNPCEpiC	eye:	n/a
24	chr4:88340947-88340997	AG09309	skin:	n/a
25	chr4:88340947-88340997	CMK	blood:	n/a
26	chr4:88340947-88340997	ProgFib	skin:	n/a
27	chr4:88340947-88340997	Hepatocyte	liver:	n/a
28	chr4:88340947-88340997	SAEC	small airway:	n/a
29	chr4:88340947-88340997	PANC-1	pancreas:	n/a
30	chr4:88340947-88340997	A549	lung:	n/a
31	chr4:88340947-88340997	Jurkat	blood:	n/a
32	chr4:88340947-88340997	GM12891	blood:	n/a
33	chr4:88340947-88340997	AG09319	gingival:	n/a
34	chr4:88340947-88340997	HMEC	breast:	n/a
35	chr4:88340947-88340997	T-47D	breast:	n/a
36	chr4:88340947-88340997	HRE	kidney:	n/a
37	chr4:88340947-88340997	NT2-D1	testis:	n/a
38	chr4:88340947-88340997	GM12878	blood:	n/a
39	chr4:88340947-88340997	HCPEpiC	choroid plexus:	n/a
40	chr4:88340947-88340997	HCT-116	colon:	n/a
41	chr4:88340947-88340997	HPAEpiC	pulmonary alveolar:	n/a
42	chr4:88340947-88340997	HRPEpiC	eye:	n/a
43	chr4:88340947-88340997	HRCEpiC	kidney:	n/a
44	chr4:88340947-88340997	HCF	heart:	n/a
45	chr4:88340947-88340997	NH-A	brain:	n/a
46	chr4:88340947-88340997	H1-hESC	embryonic stem cell:	embryo
47	chr4:88340947-88340997	AG04449	skin:	fetal
48	chr4:88340947-88340997	HAEpiC	amniotic membrane:	n/a
49	chr4:88340947-88340997	HEEpiC	esophagus:	n/a
50	chr4:88340947-88340997	GM12892	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
2	chr4:88340622..88342394-chr4:88382444..88384320,2	MCF-7	breast:
3	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:

Variant related genes	Relation type
NUDT9	TF binding region
NUDT9	CpG island
ENSG00000272856	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10010988	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10025902	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032597	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11945232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103927	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13104303	0.81[MEX][hapmap]
rs13113575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13130945	0.81[AMR][1000 genomes]
rs13138404	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]
rs13138636	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]
rs13150578	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28372775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406846	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502849	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609242	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28630962	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28701008	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28736552	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34549877	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322242	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35371368	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35649088	0.81[AMR][1000 genomes]
rs4324526	0.81[MEX][hapmap]
rs6816224	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7659182	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9654159	0.81[AMR][1000 genomes]
rs9654160	0.81[AMR][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
rs4314250	HSD17B13	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88329600-88342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:88334600-88342800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:88339400-88343000	Enhancers	Fetal Intestine Large	intestine
4	chr4:88340000-88343000	Enhancers	Fetal Intestine Small	intestine
5	chr4:88340000-88343000	Enhancers	Pancreas	Pancrea
6	chr4:88340400-88341400	Weak transcription	Small Intestine	intestine
7	chr4:88340400-88341400	Enhancers	HUVEC	blood vessel
8	chr4:88340400-88342000	Enhancers	Stomach Mucosa	stomach
9	chr4:88340400-88343000	Enhancers	Duodenum Mucosa	Duodenum
10	chr4:88340600-88341000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr4:88340600-88341000	Enhancers	NH-A	brain
12	chr4:88340600-88341200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr4:88340600-88341400	Flanking Active TSS	Liver	Liver
14	chr4:88340600-88341800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr4:88340600-88342600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:88340600-88342600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:88340800-88341200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:88340800-88341200	Enhancers	HepG2	liver
19	chr4:88340800-88341400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr4:88340800-88341400	Flanking Active TSS	A549	lung
21	chr4:88340800-88342200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:88340800-88342400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:88340800-88342400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:88340800-88342600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr4:88340800-88342600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr4:88340800-88342600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr4:88340800-88342600	Enhancers	Fetal Kidney	kidney
28	chr4:88340800-88342800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:88340800-88343000	Weak transcription	Colonic Mucosa	Colon
30	chr4:88340800-88343200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:88340800-88343200	Weak transcription	Gastric	stomach

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