Variant report

Variant	rs4131080
Chromosome Location	chr5:179044292-179044293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

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	chr5:179043923-179044328	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:179032268-179046451	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:179042826-179046520	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:179042648-179045470	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:179043741-179045403	GM12891	blood:	n/a	n/a
9	POLR2A	chr5:179043857-179046487	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:179044211-179045646	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr5:179043926-179046411	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:179044191-179045444	K562	blood:	n/a	n/a
13	POLR2A	chr5:179043797-179046611	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:179039431-179049902	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:179041696-179046640	K562	blood:	n/a	n/a
16	POLR2A	chr5:179042278-179046065	U87	brain:	n/a	n/a
17	POLR2A	chr5:179044280-179045500	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr5:179042778-179046466	K562	blood:	n/a	n/a
19	POLR2A	chr5:179044291-179046579	U87	brain:	n/a	n/a
20	POLR2A	chr5:179044175-179045434	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr5:179036095-179046498	GM12891	blood:	n/a	n/a
22	POLR2A	chr5:179044291-179045990	U87	brain:	n/a	n/a
23	POLR2A	chr5:179043809-179045917	GM12892	blood:	n/a	n/a
24	POLR2A	chr5:179043848-179051855	MCF-7	breast:	n/a	n/a
25	POLR2A	chr5:179041593-179046548	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr5:179043735-179046582	GM12892	blood:	n/a	n/a
27	POLR2A	chr5:179044231-179045366	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr5:179044266-179044687	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr5:179044287-179046095	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr5:179030899-179046584	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr5:179044048-179046113	U87	brain:	n/a	n/a
32	POLR2A	chr5:179043859-179046706	K562	blood:	n/a	n/a
33	POLR2A	chr5:179044274-179045325	GM12892	blood:	n/a	n/a
34	POLR2A	chr5:179043771-179045478	GM12891	blood:	n/a	n/a
35	POLR2A	chr5:179033822-179051830	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr5:179036058-179051879	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
HNRNPH1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10054335	0.81[ASN][1000 genomes]
rs10056863	0.81[CHD][hapmap]
rs10066669	0.88[ASN][1000 genomes]
rs10076293	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1136267	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12658664	0.85[CEU][hapmap];0.80[GIH][hapmap];0.83[TSI][hapmap]
rs17052462	0.85[ASN][1000 genomes]
rs28544040	0.88[ASN][1000 genomes]
rs4078141	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4256313	0.81[ASN][1000 genomes]
rs4376229	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701132	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4701143	0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6601050	0.85[CEU][hapmap]
rs6876679	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6895677	0.81[CHD][hapmap]
rs7448707	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs7702303	0.85[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs7703730	0.85[CEU][hapmap]
rs7706275	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4131080	RUFY1	cis	parietal	SCAN
rs4131080	HNRPH1	cis	multi-tissue	Pritchard
rs4131080	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs4131080	HNRNPH1	cis	Lymphoblastoid	GTEx
rs4131080	HNRNPH1	cis	parietal	SCAN
rs4131080	RUFY1	cis	cerebellum	SCAN
rs4131080	HNRNPH1	cis	lymphoblastoid	seeQTL

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	chr5:179007400-179045000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:179011000-179045600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:179012600-179047000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr5:179013800-179044800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:179014000-179044400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179014000-179046000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:179016200-179045000	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr5:179025200-179045000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:179028200-179046200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:179028400-179046000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:179028600-179046200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:179028800-179045000	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr5:179029200-179045600	Strong transcription	Primary B cells from cord blood	blood
17	chr5:179031000-179045600	Strong transcription	Osteobl	bone
18	chr5:179031000-179046200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:179032200-179045800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:179032200-179046400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:179032400-179045600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:179032400-179047400	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr5:179032800-179045000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:179033600-179046000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr5:179034200-179046600	Strong transcription	Colonic Mucosa	Colon
26	chr5:179035200-179044400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:179035200-179045200	Strong transcription	Fetal Brain Female	brain
28	chr5:179035600-179045000	Strong transcription	Brain Substantia Nigra	brain
29	chr5:179035600-179045000	Strong transcription	Thymus	Thymus
30	chr5:179035600-179045200	Strong transcription	Brain Hippocampus Middle	brain
31	chr5:179035800-179046200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr5:179036000-179045200	Strong transcription	NHEK	skin
33	chr5:179036000-179046000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:179036200-179045200	Strong transcription	Brain Angular Gyrus	brain
35	chr5:179036400-179044800	Strong transcription	HMEC	breast
36	chr5:179036400-179046200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:179036800-179044400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr5:179036800-179044800	Genic enhancers	K562	blood
39	chr5:179036800-179045000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:179036800-179045600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr5:179036800-179046200	Strong transcription	HSMMtube	muscle
42	chr5:179037000-179044800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr5:179037000-179045600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:179037200-179046000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:179037200-179046000	Strong transcription	Ovary	ovary
46	chr5:179037400-179045800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:179037600-179044600	Genic enhancers	A549	lung
48	chr5:179037600-179045800	Strong transcription	Brain Anterior Caudate	brain
49	chr5:179037600-179046400	Strong transcription	Spleen	Spleen
50	chr5:179037800-179044400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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