Variant report

Variant	rs4840132
Chromosome Location	chr6:100914602-100914603
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	SIN3A	chr6:100914320-100915147	H1-hESC	embryonic stem cell:	n/a	chr6:100914860-100914873 chr6:100914860-100914871
2	POLR2A	chr6:100912882-100916388	H1-neurons	neurons:	n/a	n/a
3	SUZ12	chr6:100910832-100914607	NT2-D1	testis:	n/a	n/a
4	SUZ12	chr6:100912951-100915101	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr6:100914497-100914775	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr6:100914489-100914933	H1-hESC	embryonic stem cell:	n/a	chr6:100914855-100914869 chr6:100914737-100914751
7	POLR2A	chr6:100912776-100916575	H1-neurons	neurons:	n/a	n/a
8	E2F6	chr6:100914596-100915415	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:100908327..100910621-chr6:100914553..100916127,2	MCF-7	breast:
2	chr6:100887185..100889268-chr6:100914294..100916955,2	MCF-7	breast:
3	chr6:100914205..100915074-chr6:100925463..100926076,2	MCF-7	breast:

Variant related genes	Relation type
SIM1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10457800	0.86[EUR][1000 genomes]
rs11155472	0.87[EUR][1000 genomes]
rs11155477	0.86[EUR][1000 genomes]
rs12208241	0.86[EUR][1000 genomes]
rs12212939	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12664707	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13201976	0.86[EUR][1000 genomes]
rs1894561	0.92[EUR][1000 genomes]
rs2007134	0.93[EUR][1000 genomes]
rs2071826	0.92[EUR][1000 genomes]
rs2157342	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2213594	0.86[EUR][1000 genomes]
rs2213595	0.92[EUR][1000 genomes]
rs2397974	0.93[EUR][1000 genomes]
rs241816	0.81[GIH][hapmap]
rs241819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839780	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs4840133	0.89[EUR][1000 genomes]
rs4840134	0.89[EUR][1000 genomes]
rs6901854	0.94[EUR][1000 genomes]
rs6903206	0.86[EUR][1000 genomes]
rs6910391	0.87[EUR][1000 genomes]
rs6929748	0.92[EUR][1000 genomes]
rs6939998	0.86[EUR][1000 genomes]
rs7748269	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7751185	0.91[EUR][1000 genomes]
rs7751526	0.91[EUR][1000 genomes]
rs7773043	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7773661	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322076	0.89[EUR][1000 genomes]
rs9373504	0.92[EUR][1000 genomes]
rs9386154	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100908000-100914800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:100911800-100916000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr6:100912200-100915800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:100913200-100914800	Weak transcription	Gastric	stomach
5	chr6:100913400-100915200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
6	chr6:100913400-100915600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr6:100913800-100916000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr6:100914000-100915200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:100914200-100914800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:100914200-100915200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:100914400-100914800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:100914400-100914800	Bivalent Enhancer	Fetal Stomach	stomach
13	chr6:100914400-100915000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:100914400-100915000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:100914400-100915000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
16	chr6:100914400-100915000	Bivalent Enhancer	NH-A	brain
17	chr6:100914400-100915200	Bivalent Enhancer	Colon Smooth Muscle	Colon
18	chr6:100914400-100915600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr6:100914400-100915600	Bivalent Enhancer	Esophagus	oesophagus
20	chr6:100914400-100915800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr6:100914400-100915800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr6:100914400-100915800	Bivalent Enhancer	Fetal Thymus	thymus
23	chr6:100914600-100914800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:100914600-100914800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
25	chr6:100914600-100914800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:100914600-100915000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
27	chr6:100914600-100915000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr6:100914600-100915000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:100914600-100915000	Bivalent Enhancer	Fetal Intestine Large	intestine
30	chr6:100914600-100915000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr6:100914600-100915000	Bivalent/Poised TSS	Right Ventricle	heart
32	chr6:100914600-100915200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:100914600-100915200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr6:100914600-100915200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr6:100914600-100915400	Bivalent Enhancer	Liver	Liver
36	chr6:100914600-100915400	Bivalent Enhancer	HepG2	liver
37	chr6:100914600-100915600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
38	chr6:100914600-100915800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:100914600-100916200	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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