Variant report

Variant	rs2287734
Chromosome Location	chr19:39100594-39100595
allele	C/T
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	chr19:39100215-39100900	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:39100061-39100606	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39098771..39100599-chr19:39103260..39105890,2	MCF-7	breast:
2	chr19:39086053..39087682-chr19:39099165..39101048,2	K562	blood:
3	chr19:39096157..39098643-chr19:39100433..39102103,2	MCF-7	breast:

Variant related genes	Relation type
MAP4K1	TF binding region
ENSG00000267291	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1004795	1.00[CEU][hapmap]
rs1004796	1.00[CEU][hapmap]
rs10404936	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs10405232	1.00[YRI][hapmap]
rs10405261	1.00[YRI][hapmap]
rs10408694	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs10408718	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10413936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10420476	1.00[YRI][hapmap]
rs10421560	1.00[YRI][hapmap]
rs12459780	1.00[CEU][hapmap]
rs12461431	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12461789	1.00[CEU][hapmap]
rs13344413	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs13345914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468570	0.83[AFR][1000 genomes]
rs17847678	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1966386	1.00[AFR][1000 genomes]
rs1978444	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2098657	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292800	1.00[CEU][hapmap]
rs2292801	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2303040	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2303041	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2368477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437841	0.83[AFR][1000 genomes]
rs3786830	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs3786839	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3786844	1.00[TSI][hapmap]
rs4801804	1.00[AFR][1000 genomes]
rs4802582	1.00[CEU][hapmap]
rs4802583	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4802584	1.00[CEU][hapmap]
rs4802589	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4802618	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs55922338	0.80[AMR][1000 genomes]
rs59727665	1.00[EUR][1000 genomes]
rs6508809	1.00[CEU][hapmap]
rs7251903	1.00[YRI][hapmap]
rs73552634	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750437	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];1.00[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	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
8	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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39074800-39101600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr19:39077000-39101600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:39077200-39103200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr19:39087200-39107800	Weak transcription	Colonic Mucosa	Colon
5	chr19:39087400-39107400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr19:39087400-39108200	Weak transcription	Gastric	stomach
7	chr19:39087400-39108800	Weak transcription	Right Atrium	heart
8	chr19:39092600-39109000	Weak transcription	Small Intestine	intestine
9	chr19:39094000-39104600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:39094200-39104200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:39094400-39104200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr19:39094400-39105000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr19:39094600-39104000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:39094600-39104400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:39094600-39106200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:39094800-39103400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:39094800-39104000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:39094800-39106400	Strong transcription	Primary T cells from cord blood	blood
19	chr19:39095400-39104400	Strong transcription	Thymus	Thymus
20	chr19:39095600-39104800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:39095600-39106000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr19:39095800-39106000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:39096200-39102400	Strong transcription	Spleen	Spleen
24	chr19:39096200-39104000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:39096200-39105200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:39096600-39102600	Strong transcription	Dnd41	blood
27	chr19:39096800-39108000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:39097600-39101600	Weak transcription	Fetal Thymus	thymus
29	chr19:39097800-39101600	Weak transcription	Primary B cells from cord blood	blood
30	chr19:39097800-39103200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:39097800-39108200	Weak transcription	Fetal Intestine Small	intestine
32	chr19:39098400-39104200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr19:39098600-39108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:39100000-39103600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:39100200-39103600	Strong transcription	GM12878-XiMat	blood
36	chr19:39100200-39104200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:39100400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:39100400-39104200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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