Variant report

Variant	rs12109442
Chromosome Location	chr5:95163635-95163636
allele	A/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	TAL1	chr5:95163270-95163678	K562	blood:	n/a	n/a
2	RCOR1	chr5:95163568-95163735	K562	blood:	n/a	n/a
3	GATA1	chr5:95162784-95163834	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95162262..95164257-chr5:95169999..95171533,2	MCF-7	breast:
2	chr5:95156277..95158130-chr5:95161683..95164482,2	K562	blood:

Variant related genes	Relation type
GLRX	TF binding region
ENSG00000251000	Chromatin interaction
ENSG00000173221	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10040697	0.85[CHB][hapmap]
rs12109499	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12651950	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12658997	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17085159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs17085165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085170	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2007	0.82[CHB][hapmap]
rs2546193	0.85[CHB][hapmap]
rs3822751	0.95[CHB][hapmap]
rs4869251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59044001	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60682160	0.83[ASN][1000 genomes]
rs6556883	1.00[CHB][hapmap]
rs72656688	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7734301	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv462255	chr5:95142817-95168155	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv598961	chr5:95142817-95168155	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95158800-95164800	Enhancers	Fetal Intestine Large	intestine
2	chr5:95159800-95164800	Enhancers	Fetal Intestine Small	intestine
3	chr5:95159800-95169800	Weak transcription	Fetal Kidney	kidney
4	chr5:95160200-95164800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:95160200-95169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:95160600-95168800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:95160600-95170000	Weak transcription	Right Atrium	heart
8	chr5:95160600-95170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:95160800-95166400	Weak transcription	Gastric	stomach
10	chr5:95160800-95168000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:95160800-95168200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:95160800-95168800	Weak transcription	Placenta	Placenta
13	chr5:95160800-95169000	Weak transcription	Psoas Muscle	Psoas
14	chr5:95160800-95169800	Weak transcription	Fetal Heart	heart
15	chr5:95160800-95169800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:95161400-95163800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:95161400-95168400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:95161600-95171400	Weak transcription	Small Intestine	intestine
19	chr5:95161800-95163800	Weak transcription	Spleen	Spleen
20	chr5:95161800-95164400	Weak transcription	Pancreas	Pancrea
21	chr5:95161800-95165000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:95161800-95165200	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:95161800-95168000	Weak transcription	GM12878-XiMat	blood
24	chr5:95161800-95168800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:95161800-95169800	Weak transcription	Thymus	Thymus
26	chr5:95161800-95170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:95162000-95168000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:95162000-95168200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:95162200-95164000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:95162400-95164600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:95162400-95168000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:95162400-95169600	Weak transcription	Hela-S3	cervix
33	chr5:95162600-95164400	Enhancers	Primary B cells from cord blood	blood
34	chr5:95162800-95163800	Enhancers	Adipose Nuclei	Adipose
35	chr5:95162800-95163800	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr5:95162800-95164200	Enhancers	Stomach Mucosa	stomach
37	chr5:95162800-95164400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr5:95162800-95164400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr5:95162800-95164800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr5:95163000-95164200	Enhancers	A549	lung
41	chr5:95163000-95164400	Enhancers	Liver	Liver
42	chr5:95163000-95164800	Enhancers	Lung	lung
43	chr5:95163200-95164000	Enhancers	Primary T cells from cord blood	blood
44	chr5:95163200-95164600	Enhancers	Fetal Thymus	thymus
45	chr5:95163400-95163800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:95163400-95164800	Enhancers	Colonic Mucosa	Colon
47	chr5:95163400-95164800	Enhancers	HepG2	liver
48	chr5:95163600-95163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:95163600-95164000	Enhancers	Dnd41	blood
50	chr5:95163600-95164000	Flanking Active TSS	K562	blood

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