Variant report

Variant	rs6453232
Chromosome Location	chr5:75860695-75860696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75854326..75856350-chr5:75859586..75862495,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10041515	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10043064	0.87[AMR][1000 genomes]
rs10044679	0.84[AMR][1000 genomes]
rs10044688	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10051729	0.92[AMR][1000 genomes]
rs10054114	0.80[AMR][1000 genomes]
rs10064543	0.84[JPT][hapmap]
rs10065424	0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10073592	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10080190	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10474482	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10942784	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12513951	0.84[JPT][hapmap]
rs13355881	0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1501690	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2047731	0.80[AMR][1000 genomes]
rs2134190	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2173926	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2202113	0.84[JPT][hapmap]
rs2202114	0.84[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2840106	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3776768	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3822528	0.81[TSI][hapmap]
rs4235700	0.80[AMR][1000 genomes]
rs4704326	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4704330	0.89[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704332	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4704333	0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4704336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6453231	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6869692	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7707801	0.80[GIH][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs7713954	0.84[AMR][1000 genomes]
rs905162	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs905163	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs905164	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9293687	0.93[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9654416	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9686939	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6453232	GFM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75843800-75884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:75845400-75876600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:75851600-75861200	Weak transcription	Thymus	Thymus
6	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:75852000-75864400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:75852800-75877800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:75852800-75877800	Weak transcription	Small Intestine	intestine
10	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:75854600-75863000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr5:75855800-75862400	Weak transcription	Fetal Thymus	thymus
13	chr5:75856400-75873000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:75856600-75861600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:75857000-75863200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:75857200-75863200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:75857400-75862000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:75857400-75866200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:75857600-75861400	Weak transcription	K562	blood
20	chr5:75857600-75863200	Weak transcription	Gastric	stomach
21	chr5:75857600-75863800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr5:75857600-75864000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:75857800-75863800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:75858000-75864000	Strong transcription	Primary B cells from cord blood	blood
25	chr5:75858600-75860800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:75858600-75861200	Weak transcription	Stomach Mucosa	stomach
27	chr5:75858800-75866000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:75858800-75876600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:75859000-75866000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:75859000-75866200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:75859000-75873200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:75859000-75878600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:75859800-75863400	Strong transcription	Primary T cells from cord blood	blood
34	chr5:75859800-75864800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr5:75860000-75861200	Enhancers	Fetal Lung	lung
36	chr5:75860000-75861400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr5:75860000-75862600	Strong transcription	Liver	Liver
38	chr5:75860000-75862800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:75860200-75861000	Enhancers	Fetal Stomach	stomach
40	chr5:75860200-75861200	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr5:75860200-75861600	Enhancers	Ovary	ovary
42	chr5:75860200-75862600	Strong transcription	HepG2	liver
43	chr5:75860400-75860800	Enhancers	Lung	lung
44	chr5:75860400-75861200	Strong transcription	Pancreas	Pancrea
45	chr5:75860400-75861600	Strong transcription	Fetal Intestine Small	intestine
46	chr5:75860400-75862400	Strong transcription	Placenta	Placenta
47	chr5:75860600-75860800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr5:75860600-75860800	Enhancers	Spleen	Spleen
49	chr5:75860600-75861000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr5:75860600-75862200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links