Variant report

Variant	rs6449602
Chromosome Location	chr5:61933069-61933070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10051492	0.84[CEU][hapmap]
rs10054305	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10058044	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10058598	0.88[CHD][hapmap]
rs10060589	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10065749	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10069745	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10069988	0.88[CHD][hapmap]
rs10071568	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10072795	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516160	0.84[CEU][hapmap]
rs12517326	0.88[CHD][hapmap]
rs12521329	0.84[CEU][hapmap]
rs1301064	0.83[CHD][hapmap]
rs13167856	0.84[CEU][hapmap]
rs13174978	0.91[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1477358	0.83[CHD][hapmap]
rs149540	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs152184	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs152199	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs152215	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs153857	0.81[CEU][hapmap]
rs1541677	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562244	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs173522	0.81[CEU][hapmap]
rs181912	0.84[CEU][hapmap]
rs247229	0.81[CEU][hapmap]
rs247233	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs247237	0.83[CHD][hapmap]
rs247479	0.83[CHD][hapmap]
rs26624	0.81[CEU][hapmap]
rs26625	0.81[CEU][hapmap]
rs26628	0.81[CEU][hapmap]
rs26630	0.81[CEU][hapmap]
rs26635	0.83[CHD][hapmap]
rs26637	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs26642	0.83[CHD][hapmap]
rs26645	0.81[CEU][hapmap]
rs27448	0.83[CHD][hapmap]
rs28539215	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28581963	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32154	0.84[CEU][hapmap]
rs32155	0.84[CEU][hapmap]
rs32164	0.84[CEU][hapmap]
rs32171	0.81[CEU][hapmap]
rs32181	0.84[CEU][hapmap]
rs32186	0.81[CEU][hapmap]
rs32187	0.84[CEU][hapmap]
rs32188	0.84[CEU][hapmap]
rs35010	0.81[CEU][hapmap]
rs35119	0.83[CHD][hapmap]
rs366238	0.84[CEU][hapmap]
rs3776638	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs39923	0.84[CEU][hapmap]
rs39935	0.84[CEU][hapmap]
rs4700012	0.84[CEU][hapmap]
rs4700494	0.83[CHD][hapmap]
rs6449601	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6881888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6888641	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767159	0.83[CHD][hapmap]
rs7706610	0.84[CEU][hapmap]
rs7717128	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7718484	0.84[CEU][hapmap]
rs7722692	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7729526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737525	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs784916	0.83[CHD][hapmap]
rs784921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs918606	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv881731	chr5:61794164-61941043	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv881732	chr5:61811970-62063366	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv2763458	chr5:61852234-62157166	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1022817	chr5:61853619-62149259	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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
7	nsv948334	chr5:61891622-62197219	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv4858	chr5:61922306-61966961	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6449602	DIMT1L	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61848200-61939600	Weak transcription	Brain Anterior Caudate	brain
2	chr5:61864800-61945800	Weak transcription	HSMMtube	muscle
3	chr5:61881400-61939400	Weak transcription	Spleen	Spleen
4	chr5:61886800-61941200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:61888800-61937000	Weak transcription	Gastric	stomach
6	chr5:61889600-61936200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:61893000-61943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:61899800-61939600	Weak transcription	Pancreas	Pancrea
9	chr5:61902000-61934200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:61905400-61939200	Weak transcription	Fetal Kidney	kidney
11	chr5:61906000-61946000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:61911000-61933800	Weak transcription	Aorta	Aorta
13	chr5:61911000-61939200	Weak transcription	Fetal Stomach	stomach
14	chr5:61911000-61944200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:61911200-61941800	Weak transcription	Fetal Intestine Small	intestine
16	chr5:61913400-61943000	Weak transcription	Hela-S3	cervix
17	chr5:61917200-61945800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:61920400-61942600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:61923000-61945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:61923200-61935000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:61923200-61939000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:61923400-61941400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:61923800-61935600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:61924000-61936000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:61924000-61944400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:61924200-61935800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:61924200-61949200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:61924200-61950600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:61924600-61939600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:61925600-61933400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:61925600-61937600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:61925600-61944000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:61925600-61944800	Weak transcription	Dnd41	blood
34	chr5:61925800-61934800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:61925800-61935400	Weak transcription	K562	blood
36	chr5:61925800-61937800	Weak transcription	Primary B cells from cord blood	blood
37	chr5:61925800-61939200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:61925800-61941800	Weak transcription	A549	lung
39	chr5:61925800-61943200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:61925800-61943800	Weak transcription	Primary T cells from cord blood	blood
41	chr5:61925800-61945200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:61925800-61949200	Weak transcription	Left Ventricle	heart
43	chr5:61926000-61934400	Weak transcription	Fetal Intestine Large	intestine
44	chr5:61926200-61934400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr5:61926200-61935800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:61926600-61934200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:61926800-61934200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:61926800-61945400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:61927400-61943400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:61928400-61936000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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