Variant report

Variant	rs3761742
Chromosome Location	chr5:74678937-74678938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10038723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10043621	0.81[EUR][1000 genomes]
rs10044053	0.85[EUR][1000 genomes]
rs10053643	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10075139	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10434644	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10462517	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10473972	0.82[ASN][1000 genomes]
rs10474434	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10474436	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1051795	0.83[EUR][1000 genomes]
rs10942739	0.84[ASN][1000 genomes]
rs11957913	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12234032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354407	0.86[EUR][1000 genomes]
rs17238484	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2287711	0.84[EUR][1000 genomes]
rs28609217	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2878418	0.84[EUR][1000 genomes]
rs3213801	0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs3761743	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846666	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3931914	0.95[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs4385188	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4440336	0.85[ASN][1000 genomes]
rs4703670	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4704214	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4704228	0.84[EUR][1000 genomes]
rs57149337	0.90[ASN][1000 genomes]
rs57312935	0.86[EUR][1000 genomes]
rs5744533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744575	0.86[EUR][1000 genomes]
rs5744598	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs5744601	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs5744621	0.85[EUR][1000 genomes]
rs59506842	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61430233	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6453134	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6863398	0.89[ASN][1000 genomes]
rs6872314	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6874781	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs698912	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73120833	0.80[ASN][1000 genomes]
rs7356637	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445415	0.83[EUR][1000 genomes]
rs7700468	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7701925	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7709282	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs7732854	0.83[EUR][1000 genomes]
rs7737959	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9885386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3761742	GCNT4	cis	cerebellum	SCAN
rs3761742	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:74659800-74684800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
9	chr5:74660200-74707800	Weak transcription	Stomach Mucosa	stomach
10	chr5:74661800-74683600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:74665000-74703000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr5:74667200-74688200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:74667200-74693600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:74667600-74687600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:74668000-74688400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:74668200-74686200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:74668400-74685600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:74668600-74681600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:74668600-74686800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr5:74668600-74687200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:74668600-74687600	Strong transcription	Adipose Nuclei	Adipose
23	chr5:74668600-74687600	Strong transcription	Fetal Lung	lung
24	chr5:74668600-74691200	Strong transcription	Liver	Liver
25	chr5:74668800-74685800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr5:74669600-74681400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:74670800-74709400	Weak transcription	Pancreas	Pancrea
28	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
29	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:74671000-74686000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:74671000-74722800	Weak transcription	Hela-S3	cervix
32	chr5:74671600-74686000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr5:74671800-74684200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr5:74672000-74682000	Strong transcription	Primary B cells from cord blood	blood
35	chr5:74672200-74687000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr5:74673000-74682400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:74673200-74682600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:74673200-74685200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:74673200-74685800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:74673200-74685800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:74673200-74685800	Strong transcription	Dnd41	blood
42	chr5:74673200-74686000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:74673400-74682200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:74673400-74685800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr5:74673400-74686000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:74673600-74681400	Strong transcription	Placenta	Placenta
47	chr5:74673600-74681600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:74674400-74688000	Weak transcription	NHEK	skin
49	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
50	chr5:74674800-74679000	Strong transcription	HSMM	muscle

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