Variant report

Variant	rs351769
Chromosome Location	chr5:112199974-112199975
allele	A/G
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	POLR2A	chr5:112199585-112201114	K562	blood:	n/a	n/a
2	POLR2A	chr5:112199905-112200052	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:112199920-112200235	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112194408..112196977-chr5:112198175..112200544,3	MCF-7	breast:
2	chr5:112195906..112198557-chr5:112198644..112200582,4	MCF-7	breast:
3	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
4	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:

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

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1069061	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1093611	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1093677	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12656359	0.80[ASN][1000 genomes]
rs1441375	0.84[CEU][hapmap]
rs149192	0.90[JPT][hapmap]
rs151976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151977	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151978	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153545	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153546	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs153548	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1661035	0.84[CEU][hapmap]
rs193527	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1966477	0.82[ASN][1000 genomes]
rs2545162	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs2545163	0.83[CEU][hapmap]
rs2545165	0.90[JPT][hapmap]
rs2545166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2545167	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2545169	0.83[CEU][hapmap]
rs2909786	0.90[JPT][hapmap]
rs2909787	0.90[JPT][hapmap]
rs2909904	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909958	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2952615	0.90[JPT][hapmap]
rs351767	0.99[EUR][1000 genomes]
rs351770	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs351771	0.90[JPT][hapmap]
rs35726351	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368575	0.82[JPT][hapmap]
rs372492	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs380144	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs382260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386830	0.92[ASN][1000 genomes]
rs392907	0.84[CEU][hapmap]
rs397768	0.89[ASN][1000 genomes]
rs41115	0.90[JPT][hapmap]
rs411356	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs419632	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42427	0.90[JPT][hapmap]
rs429427	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430665	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs433429	0.92[ASN][1000 genomes]
rs434090	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434157	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs438252	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs439456	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442507	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs446567	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454968	0.81[EUR][1000 genomes]
rs455412	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs455469	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs456313	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs458451	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs459102	0.85[EUR][1000 genomes]
rs460301	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460832	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs461424	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs461866	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs463229	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464002	0.84[CEU][hapmap]
rs464708	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs465454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs465899	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs466443	0.93[CHB][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs468101	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs468610	0.81[EUR][1000 genomes]
rs468783	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468854	0.82[EUR][1000 genomes]
rs469663	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469727	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs469827	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs481789	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs495794	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs497844	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs514763	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs519397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs563556	0.80[CEU][hapmap]
rs565453	0.93[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs565603	0.94[ASN][1000 genomes]
rs580237	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698405	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712662	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712663	0.83[EUR][1000 genomes]
rs712664	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712665	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712666	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712668	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712671	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs818423	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs818424	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs818425	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs818426	0.88[ASN][1000 genomes]
rs818427	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs818429	0.85[EUR][1000 genomes]
rs818782	0.83[ASN][1000 genomes]
rs864682	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9011	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][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
rs351769	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs351769	REEP5	cis	uninvolved skin	skin_eQTL

Chromatin state (count:126 , 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	chr5:112198000-112200000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:112198000-112205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:112198200-112200200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
6	chr5:112198200-112202200	Weak transcription	Fetal Kidney	kidney
7	chr5:112198400-112200000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:112198400-112200000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr5:112198400-112200000	Enhancers	Brain Cingulate Gyrus	brain
10	chr5:112198400-112200000	Weak transcription	Colonic Mucosa	Colon
11	chr5:112198400-112200200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:112198400-112200200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:112198400-112200400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:112198400-112200800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:112198600-112200000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:112198600-112200600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:112198600-112201000	Genic enhancers	Osteobl	bone
20	chr5:112198600-112201200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:112198600-112205600	Weak transcription	Fetal Brain Male	brain
22	chr5:112198600-112206600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:112198600-112206800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr5:112198600-112206800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:112198600-112206800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr5:112198600-112207000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr5:112198600-112207000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:112198600-112207400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr5:112198600-112208800	Strong transcription	Fetal Thymus	thymus
30	chr5:112198800-112200000	Genic enhancers	Primary T cells from cord blood	blood
31	chr5:112198800-112200000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:112198800-112200000	Genic enhancers	Liver	Liver
33	chr5:112198800-112206800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:112198800-112206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:112198800-112207200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr5:112198800-112208800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:112199000-112200000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:112199000-112200000	Genic enhancers	Brain Hippocampus Middle	brain
39	chr5:112199000-112200000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:112199000-112200000	Genic enhancers	HUVEC	blood vessel
41	chr5:112199000-112200000	Genic enhancers	NHLF	lung
42	chr5:112199000-112200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:112199000-112200600	Strong transcription	Thymus	Thymus
44	chr5:112199000-112200800	Strong transcription	Ovary	ovary
45	chr5:112199000-112201200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr5:112199000-112201200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr5:112199000-112206800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:112199000-112207000	Strong transcription	Placenta	Placenta
49	chr5:112199000-112207200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:112199000-112208000	Strong transcription	Primary B cells from peripheral blood	blood

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