Variant report

Variant	rs10065424
Chromosome Location	chr5:75841888-75841889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75628819..75631136-chr5:75840007..75842103,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10041515	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10043064	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10044679	0.87[AMR][1000 genomes]
rs10044688	0.88[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10051729	0.87[AMR][1000 genomes]
rs10054114	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10064543	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs10073592	0.83[AMR][1000 genomes]
rs10080190	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10474482	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10942784	0.88[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12513951	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13355881	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]
rs1501690	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2047731	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2134190	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2173926	0.81[EUR][1000 genomes]
rs2202113	0.89[JPT][hapmap]
rs2202114	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840106	0.83[EUR][1000 genomes]
rs2884654	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3776768	0.81[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs3797380	0.88[JPT][hapmap]
rs4235700	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4437351	0.83[AMR][1000 genomes]
rs4704326	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4704330	0.81[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704333	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704336	0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6453231	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6453232	0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6869692	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6889411	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7707801	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713954	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7722711	0.94[JPT][hapmap]
rs905162	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs905163	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs905164	0.81[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9293687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9293688	0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs9654416	0.81[AMR][1000 genomes]
rs9686939	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[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
rs10065424	GFM2	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75837400-75842800	Enhancers	Liver	Liver
3	chr5:75839400-75842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:75839400-75842400	Weak transcription	Adipose Nuclei	Adipose
5	chr5:75839400-75842600	Weak transcription	Thymus	Thymus
6	chr5:75839600-75845400	Enhancers	HepG2	liver
7	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:75839800-75842200	Enhancers	GM12878-XiMat	blood
10	chr5:75840000-75842400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:75840000-75842600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr5:75840200-75842200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:75840200-75842400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:75840200-75842400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:75840200-75842400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:75840200-75842400	Weak transcription	Colonic Mucosa	Colon
17	chr5:75840200-75842400	Weak transcription	Fetal Stomach	stomach
18	chr5:75840200-75842400	Weak transcription	Gastric	stomach
19	chr5:75840200-75842400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:75840200-75842400	Weak transcription	Small Intestine	intestine
21	chr5:75840200-75842600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr5:75840200-75842800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:75840200-75842800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr5:75840200-75842800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr5:75840200-75842800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:75840200-75842800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:75840200-75843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:75840400-75842000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr5:75840400-75842000	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:75840400-75842200	Weak transcription	Fetal Thymus	thymus
31	chr5:75840400-75842400	Weak transcription	Lung	lung
32	chr5:75840400-75842400	Weak transcription	Spleen	Spleen
33	chr5:75840400-75842800	Enhancers	Primary hematopoietic stem cells	blood
34	chr5:75840400-75843000	Weak transcription	Fetal Intestine Large	intestine
35	chr5:75840400-75843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:75840600-75842000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr5:75840600-75842200	Weak transcription	Primary T cells from cord blood	blood
38	chr5:75840600-75842200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr5:75840600-75842200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr5:75840600-75842200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:75840600-75842400	Weak transcription	Fetal Kidney	kidney
42	chr5:75840600-75842600	Weak transcription	Fetal Lung	lung
43	chr5:75840600-75843000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:75841000-75843200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:75841200-75842200	Weak transcription	Pancreas	Pancrea
46	chr5:75841200-75842400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:75841200-75842400	Weak transcription	Placenta	Placenta
48	chr5:75841200-75842400	Weak transcription	K562	blood
49	chr5:75841200-75842600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:75841200-75843000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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