Variant report

Variant	rs3786845
Chromosome Location	chr19:39195083-39195084
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39194041-39195682	K562	blood:	n/a	n/a
2	POLR2A	chr19:39194908-39195919	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:39194739-39195365	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:39194789-39196472	K562	blood:	n/a	n/a
5	POLR2A	chr19:39194197-39195652	K562	blood:	n/a	n/a
6	POLR2A	chr19:39194774-39195155	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr19:39194319-39195484	K562	blood:	n/a	n/a
8	POLR2A	chr19:39194142-39196512	K562	blood:	n/a	n/a
9	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39194344-39197081	A549	lung:	n/a	n/a
11	POLR2A	chr19:39194180-39195254	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39138096..39140426-chr19:39194942..39197534,2	K562	blood:
2	chr19:39145602..39147315-chr19:39192436..39195321,2	K562	blood:
3	chr19:39190667..39192655-chr19:39192887..39195518,3	MCF-7	breast:
4	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
5	chr19:39193469..39195241-chr19:39198344..39201605,3	K562	blood:
6	chr19:39156320..39158010-chr19:39194511..39197034,2	MCF-7	breast:
7	chr19:39127575..39128125-chr19:39194988..39195741,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACTN4	TF binding region
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403540	0.95[CHB][hapmap];0.80[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10406778	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10415219	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10415646	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421560	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426809	0.81[CHD][hapmap]
rs11083475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12460849	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12462270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13343794	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13344413	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs16972767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279144	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs28488032	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28624276	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786837	0.84[EUR][1000 genomes]
rs3786839	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3786848	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810341	0.83[ASN][1000 genomes]
rs55876653	0.82[ASN][1000 genomes]
rs55945853	0.85[EUR][1000 genomes]
rs56113315	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56365761	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120083	0.85[EUR][1000 genomes]
rs62121814	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62121816	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62121818	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes]
rs7252589	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7254100	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8107416	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs8111746	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs883394	0.97[EUR][1000 genomes]
rs883433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs979971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs979972	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3786845	PSG3	cis	parietal	SCAN
rs3786845	ZNF526	cis	cerebellum	SCAN
rs3786845	MEGF8	cis	parietal	SCAN
rs3786845	RPS16	cis	parietal	SCAN
rs3786845	LGALS17A	cis	cerebellum	SCAN
rs3786845	TMEM145	cis	parietal	SCAN
rs3786845	ERCC1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
3	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
5	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
7	chr19:39184800-39205800	Genic enhancers	A549	lung
8	chr19:39185200-39205800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:39187000-39196600	Weak transcription	Psoas Muscle	Psoas
11	chr19:39187200-39201200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
12	chr19:39187200-39205800	Genic enhancers	Right Ventricle	heart
13	chr19:39187800-39198600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:39189600-39196000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:39189800-39198200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:39190000-39203800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr19:39190000-39205800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:39190000-39208800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:39190000-39218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:39190400-39206000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:39190400-39208400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:39190400-39209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:39190400-39212000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:39190400-39212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:39190400-39217000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:39190400-39218000	Strong transcription	Primary T cells from cord blood	blood
31	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:39190400-39222600	Strong transcription	Dnd41	blood
33	chr19:39190600-39199800	Strong transcription	NHEK	skin
34	chr19:39190600-39202800	Strong transcription	GM12878-XiMat	blood
35	chr19:39190600-39203200	Strong transcription	K562	blood
36	chr19:39190600-39205400	Genic enhancers	Spleen	Spleen
37	chr19:39190600-39205600	Strong transcription	Fetal Brain Female	brain
38	chr19:39190600-39209000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:39190600-39209200	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr19:39190600-39216400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr19:39190600-39217000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:39190600-39219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:39190800-39195400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:39190800-39196600	Strong transcription	HUVEC	blood vessel
46	chr19:39190800-39220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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