Variant report

Variant	rs4701143
Chromosome Location	chr5:179045142-179045143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179039513-179045860	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:179043779-179045406	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:179041511-179046664	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:179032268-179046451	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:179042826-179046520	HepG2	liver:	n/a	n/a
6	MBD4	chr5:179045002-179045501	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:179042648-179045470	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:179045040-179045295	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:179044698-179045384	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr5:179043741-179045403	GM12891	blood:	n/a	n/a
11	POLR2A	chr5:179045047-179045374	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr5:179043857-179046487	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:179045055-179045261	A549	lung:	n/a	n/a
14	POLR2A	chr5:179044211-179045646	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr5:179044767-179045358	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr5:179044351-179045374	GM12891	blood:	n/a	n/a
17	POLR2A	chr5:179043926-179046411	HepG2	liver:	n/a	n/a
18	POLR2A	chr5:179044732-179045362	HL-60	blood:	n/a	n/a
19	HEY1	chr5:179044314-179045347	K562	blood:	n/a	n/a
20	POLR2A	chr5:179044704-179045794	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr5:179044711-179045327	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr5:179044191-179045444	K562	blood:	n/a	n/a
23	POLR2A	chr5:179045030-179045309	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:179044749-179045343	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:179044976-179045295	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:179043797-179046611	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:179044985-179045285	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr5:179039431-179049902	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:179041696-179046640	K562	blood:	n/a	n/a
30	POLR2A	chr5:179045053-179045339	HCT-116	colon:	n/a	n/a
31	WRNIP1	chr5:179045010-179045299	GM12878	blood:	n/a	n/a
32	SP1	chr5:179045018-179045373	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr5:179042278-179046065	U87	brain:	n/a	n/a
34	POLR2A	chr5:179044449-179045398	K562	blood:	n/a	n/a
35	POLR2A	chr5:179044749-179045377	K562	blood:	n/a	n/a
36	POLR2A	chr5:179044538-179045416	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr5:179044280-179045500	HUVEC	blood vessel:	n/a	n/a
38	USF2	chr5:179045096-179045244	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr5:179044395-179045467	GM12891	blood:	n/a	n/a
40	CTCF	chr5:179045100-179045250	Caco-2	colon:	n/a	n/a
41	POLR2A	chr5:179042778-179046466	K562	blood:	n/a	n/a
42	POLR2A	chr5:179044291-179046579	U87	brain:	n/a	n/a
43	POLR2A	chr5:179044388-179045809	A549	lung:	n/a	n/a
44	POLR2A	chr5:179045090-179045233	A549	lung:	n/a	n/a
45	POLR2A	chr5:179044175-179045434	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr5:179044689-179045395	K562	blood:	n/a	n/a
47	POLR2A	chr5:179036095-179046498	GM12891	blood:	n/a	n/a
48	POLR2A	chr5:179044291-179045990	U87	brain:	n/a	n/a
49	POLR2A	chr5:179044927-179045374	HCT-116	colon:	n/a	n/a
50	POLR2A	chr5:179043809-179045917	GM12892	blood:	n/a	n/a

No data

Variant related genes	Relation type
HNRNPH1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10054335	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056863	0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs11249649	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1136267	0.80[JPT][hapmap]
rs12719865	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13183244	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28639796	0.84[ASN][1000 genomes]
rs34316961	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4078141	0.80[JPT][hapmap]
rs4131080	0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4256313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4336318	0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.89[ASN][1000 genomes]
rs4376229	0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4563584	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs4608884	0.95[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs56071539	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62397276	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6601054	0.85[ASN][1000 genomes]
rs66479467	0.89[ASN][1000 genomes]
rs6895677	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7448707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7706275	0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs8087	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs8180434	0.95[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
4	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv883273	chr5:179045142-179086833	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4701143	RUFY1	cis	cerebellum	SCAN
rs4701143	HNRPH1	cis	multi-tissue	Pritchard
rs4701143	HNRNPH1	cis	lymphoblastoid	seeQTL
rs4701143	RUFY1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178987600-179045600	Strong transcription	Fetal Intestine Small	intestine
2	chr5:178987800-179045600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:179002200-179045600	Strong transcription	Fetal Intestine Large	intestine
4	chr5:179011000-179045600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:179012600-179047000	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr5:179014000-179046000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:179028200-179046200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:179028400-179046000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:179028600-179046200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:179029200-179045600	Strong transcription	Primary B cells from cord blood	blood
11	chr5:179031000-179045600	Strong transcription	Osteobl	bone
12	chr5:179031000-179046200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr5:179032200-179045800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:179032200-179046400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:179032400-179045600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:179032400-179047400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:179033600-179046000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr5:179034200-179046600	Strong transcription	Colonic Mucosa	Colon
19	chr5:179035200-179045200	Strong transcription	Fetal Brain Female	brain
20	chr5:179035600-179045200	Strong transcription	Brain Hippocampus Middle	brain
21	chr5:179035800-179046200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr5:179036000-179045200	Strong transcription	NHEK	skin
23	chr5:179036000-179046000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:179036200-179045200	Strong transcription	Brain Angular Gyrus	brain
25	chr5:179036400-179046200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:179036800-179045600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr5:179036800-179046200	Strong transcription	HSMMtube	muscle
28	chr5:179037000-179045600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:179037200-179046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:179037200-179046000	Strong transcription	Ovary	ovary
31	chr5:179037400-179045800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:179037600-179045800	Strong transcription	Brain Anterior Caudate	brain
33	chr5:179037600-179046400	Strong transcription	Spleen	Spleen
34	chr5:179037800-179045800	Genic enhancers	NHLF	lung
35	chr5:179038000-179045400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:179038600-179045600	Strong transcription	Fetal Stomach	stomach
37	chr5:179038800-179045400	Strong transcription	Fetal Brain Male	brain
38	chr5:179039200-179045600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:179039800-179046800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:179040800-179045200	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr5:179041000-179046200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:179041000-179047400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr5:179041000-179047400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr5:179041200-179045200	Strong transcription	Psoas Muscle	Psoas
45	chr5:179041200-179045400	Strong transcription	Lung	lung
46	chr5:179041200-179048600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:179041600-179046000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:179041800-179046200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr5:179042000-179046200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr5:179042200-179046400	Strong transcription	Esophagus	oesophagus

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