Variant report

Variant	rs351770
Chromosome Location	chr5:112199199-112199200
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:112199048-112199352	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:112197782-112199402	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:112198917-112199341	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:112199167-112199621	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:112198842-112199256	K562	blood:	n/a	n/a
6	POLR2A	chr5:112199011-112199436	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112196028..112199860-chr5:112256680..112260462,5	MCF-7	breast:
2	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:
3	chr5:112196670..112199465-chr5:112228539..112231018,2	K562	blood:
4	chr5:112194408..112196977-chr5:112198175..112200544,3	MCF-7	breast:
5	chr5:112195906..112198557-chr5:112198644..112200582,4	MCF-7	breast:
6	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:

No data

Variant related genes	Relation type
SRP19	TF binding region
ENSG00000272869	Chromatin interaction
ENSG00000270067	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1069061	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1093611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1093677	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs149193	0.82[ASN][1000 genomes]
rs151976	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs151977	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs151978	0.82[EUR][1000 genomes]
rs153544	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs153546	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs153548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153549	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs153550	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153551	0.89[ASN][1000 genomes]
rs153552	0.88[ASN][1000 genomes]
rs154344	0.83[ASN][1000 genomes]
rs2545155	0.84[ASN][1000 genomes]
rs2545156	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs2545165	0.85[CEU][hapmap]
rs2545166	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2545167	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2545170	0.94[ASN][1000 genomes]
rs2546108	0.85[CHB][hapmap]
rs2546112	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs2546115	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs2707765	0.80[CHB][hapmap]
rs2909904	0.86[EUR][1000 genomes]
rs2952615	0.85[CEU][hapmap]
rs3317	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs351767	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351768	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs351769	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs351771	0.84[CEU][hapmap]
rs35726351	0.88[EUR][1000 genomes]
rs368575	0.94[ASN][1000 genomes]
rs372492	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs373059	0.85[ASN][1000 genomes]
rs374613	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs380144	0.87[EUR][1000 genomes]
rs382260	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs382427	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs395858	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs410701	0.94[ASN][1000 genomes]
rs41115	0.84[CEU][hapmap]
rs41116	0.87[ASN][1000 genomes]
rs414098	0.81[CHB][hapmap]
rs419155	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs419632	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs42427	0.84[CEU][hapmap]
rs429427	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs430665	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs431287	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs434157	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs438252	0.85[EUR][1000 genomes]
rs439456	0.94[EUR][1000 genomes]
rs446567	0.83[EUR][1000 genomes]
rs448162	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs448475	0.87[ASN][1000 genomes]
rs448613	0.94[ASN][1000 genomes]
rs454968	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs455412	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs455469	0.80[EUR][1000 genomes]
rs456313	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs456531	0.91[ASN][1000 genomes]
rs458451	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs459102	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs460137	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs460301	0.87[EUR][1000 genomes]
rs460832	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes]
rs461424	0.80[EUR][1000 genomes]
rs461866	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs463229	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs465454	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs465899	0.84[CEU][hapmap]
rs468101	0.89[EUR][1000 genomes]
rs468610	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468751	0.84[ASN][1000 genomes]
rs468783	0.82[EUR][1000 genomes]
rs468854	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs469663	0.89[EUR][1000 genomes]
rs469727	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs469760	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs469827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs469886	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4705624	0.80[CHB][hapmap]
rs481789	0.87[EUR][1000 genomes]
rs495794	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497844	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs501250	0.84[CEU][hapmap]
rs505382	0.92[ASN][1000 genomes]
rs514763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs519397	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs565453	0.87[EUR][1000 genomes]
rs565603	0.87[EUR][1000 genomes]
rs566419	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs580237	0.87[EUR][1000 genomes]
rs67293732	0.91[ASN][1000 genomes]
rs698405	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs712662	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs712663	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712664	0.82[EUR][1000 genomes]
rs712665	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs712666	0.92[EUR][1000 genomes]
rs712668	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs712670	0.94[ASN][1000 genomes]
rs712671	0.95[EUR][1000 genomes]
rs7213	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs818423	0.85[EUR][1000 genomes]
rs818424	0.90[EUR][1000 genomes]
rs818425	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs818427	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs818428	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs818429	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs818430	0.91[ASN][1000 genomes]
rs818797	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs864682	0.87[EUR][1000 genomes]
rs866006	0.81[CEU][hapmap]
rs9011	0.89[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs351770	REEP5	cis	uninvolved skin	skin_eQTL
rs351770	SRP19	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112197800-112200000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr5:112197800-112211800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:112198000-112199200	Enhancers	Fetal Heart	heart
4	chr5:112198000-112199400	Enhancers	Aorta	Aorta
5	chr5:112198000-112199400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
6	chr5:112198000-112199400	Enhancers	Small Intestine	intestine
7	chr5:112198000-112200000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:112198000-112205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:112198200-112199200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:112198200-112199400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112198200-112199400	Genic enhancers	Colon Smooth Muscle	Colon
12	chr5:112198200-112199400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:112198200-112199400	Genic enhancers	Fetal Stomach	stomach
14	chr5:112198200-112199400	Transcr. at gene 5' and 3'	HSMM	muscle
15	chr5:112198200-112199600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:112198200-112199600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:112198200-112199600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr5:112198200-112199600	Transcr. at gene 5' and 3'	NH-A	brain
19	chr5:112198200-112199800	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr5:112198200-112200200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
21	chr5:112198200-112202200	Weak transcription	Fetal Kidney	kidney
22	chr5:112198400-112199200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr5:112198400-112199200	Weak transcription	Fetal Intestine Large	intestine
24	chr5:112198400-112199200	Enhancers	Psoas Muscle	Psoas
25	chr5:112198400-112199200	Genic enhancers	Monocytes-CD14+_RO01746	blood
26	chr5:112198400-112199400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:112198400-112199400	Genic enhancers	Brain Germinal Matrix	brain
28	chr5:112198400-112199400	Genic enhancers	Fetal Muscle Leg	muscle
29	chr5:112198400-112199400	Transcr. at gene 5' and 3'	A549	lung
30	chr5:112198400-112199400	Genic enhancers	HSMMtube	muscle
31	chr5:112198400-112199600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:112198400-112199600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:112198400-112199600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr5:112198400-112199600	Genic enhancers	Brain Inferior Temporal Lobe	brain
35	chr5:112198400-112199600	Enhancers	Brain Substantia Nigra	brain
36	chr5:112198400-112199800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:112198400-112199800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr5:112198400-112199800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:112198400-112200000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:112198400-112200000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr5:112198400-112200000	Enhancers	Brain Cingulate Gyrus	brain
42	chr5:112198400-112200000	Weak transcription	Colonic Mucosa	Colon
43	chr5:112198400-112200200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:112198400-112200200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:112198400-112200400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:112198400-112200800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr5:112198600-112199200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr5:112198600-112199200	Transcr. at gene 5' and 3'	Hela-S3	cervix

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