Variant report

Variant	rs13355881
Chromosome Location	chr5:75837834-75837835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10041515	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10043064	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10044679	0.89[AMR][1000 genomes]
rs10044688	0.85[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10051729	0.83[AMR][1000 genomes]
rs10054114	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10064543	0.85[CHB][hapmap]
rs10065424	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10073592	0.81[AMR][1000 genomes]
rs10080190	0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10474482	0.81[AMR][1000 genomes]
rs10942784	0.88[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12513951	0.85[CHB][hapmap]
rs1501690	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2047731	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2134190	0.81[AMR][1000 genomes]
rs2173926	0.81[EUR][1000 genomes]
rs2202114	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2884654	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3776768	0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs4235700	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704326	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4704330	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704332	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704333	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704336	0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs6453231	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6453232	0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6869692	0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6889411	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7707801	0.96[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7713954	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7722711	0.82[JPT][hapmap]
rs905162	0.81[AMR][1000 genomes]
rs905163	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs905164	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9293687	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9293688	0.85[CHB][hapmap]
rs9686939	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13355881	GFM2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75806800-75839200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:75823000-75838400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:75826800-75840000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:75828600-75839000	Weak transcription	Lung	lung
5	chr5:75829000-75838000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
7	chr5:75832200-75839000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:75832200-75840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:75832400-75838600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:75832600-75838400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:75833200-75838600	Enhancers	Duodenum Mucosa	Duodenum
12	chr5:75833400-75838400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:75833400-75838800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:75833600-75839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:75833800-75838200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr5:75833800-75838600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:75833800-75838600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:75834000-75838200	Weak transcription	Small Intestine	intestine
19	chr5:75834000-75839200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:75834200-75839000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:75834200-75839000	Enhancers	Primary hematopoietic stem cells	blood
22	chr5:75834200-75839200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:75834400-75839200	Weak transcription	Fetal Intestine Small	intestine
24	chr5:75834600-75838400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr5:75835000-75838000	Weak transcription	Fetal Thymus	thymus
26	chr5:75835000-75838400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr5:75835000-75838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:75835200-75838600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr5:75835600-75839800	Weak transcription	Spleen	Spleen
30	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:75836600-75838400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:75836600-75838400	Weak transcription	K562	blood
33	chr5:75836600-75839000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:75836600-75839200	Weak transcription	Pancreas	Pancrea
35	chr5:75836600-75839600	Weak transcription	HepG2	liver
36	chr5:75836800-75838800	Weak transcription	Gastric	stomach
37	chr5:75837000-75838600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr5:75837200-75838800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr5:75837400-75840600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr5:75837400-75842800	Enhancers	Liver	Liver
41	chr5:75837600-75838000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:75837600-75838800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:75837800-75838000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:75837800-75838800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr5:75837800-75840600	Enhancers	Fetal Lung	lung
46	chr5:75837800-75841200	Enhancers	Placenta	Placenta

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