Variant report

Variant	rs10942739
Chromosome Location	chr5:74786083-74786084
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	chr5:74773320..74775283-chr5:74785477..74788278,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10038723	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10043621	0.91[ASN][1000 genomes]
rs10044053	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10060260	0.83[EUR][1000 genomes]
rs10067641	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10070207	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10075139	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10434644	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10462517	0.89[ASN][1000 genomes]
rs10474433	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs10474436	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051795	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11957913	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12234032	0.84[ASN][1000 genomes]
rs13354407	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1427924	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17739580	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1863934	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1863935	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1995267	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2287711	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs253392	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs253393	0.95[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs253407	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs253409	0.95[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs28609217	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2878519	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2878520	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3213801	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34340	0.82[ASN][1000 genomes]
rs3761742	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]
rs3761743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846665	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs3846666	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3931914	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4045166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4385188	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4440336	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4703670	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4703674	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4704214	0.89[ASN][1000 genomes]
rs4704224	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4704228	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57149337	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57312935	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5744533	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744555	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744575	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5744595	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5744601	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5744621	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5744663	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5744703	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59506842	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61430233	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453134	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67969809	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6861279	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6863398	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6872314	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874781	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6886841	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6891949	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs698912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs73120833	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7356637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7445415	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767676	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7700468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7701925	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7706857	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709282	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717505	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7723531	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7737959	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924452	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9293656	0.85[EUR][1000 genomes]
rs9332464	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9885386	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882200	chr5:74781439-74830808	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10942739	HMGCR	cis	cerebellum	SCAN
rs10942739	COL4A3BP	cis	cerebellum	SCAN
rs10942739	S100Z	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74732000-74787400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:74742400-74794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:74760400-74792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:74762200-74805800	Weak transcription	Pancreas	Pancrea
5	chr5:74763200-74787400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:74764800-74786200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:74764800-74798600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:74765200-74795400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:74765200-74804600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:74765800-74786800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:74765800-74787200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:74767400-74787000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:74769200-74794000	Weak transcription	Fetal Thymus	thymus
14	chr5:74769400-74794800	Weak transcription	Stomach Mucosa	stomach
15	chr5:74770400-74805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:74771800-74794200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:74773200-74787800	Weak transcription	Ovary	ovary
18	chr5:74775200-74804000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:74777000-74787000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:74777000-74794200	Weak transcription	Dnd41	blood
21	chr5:74777200-74787400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:74777400-74797800	Weak transcription	Colonic Mucosa	Colon
23	chr5:74778600-74787600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:74778600-74787600	Weak transcription	Lung	lung
25	chr5:74778600-74794200	Weak transcription	Right Ventricle	heart
26	chr5:74778600-74796800	Weak transcription	Esophagus	oesophagus
27	chr5:74778600-74806400	Weak transcription	Gastric	stomach
28	chr5:74778800-74805400	Weak transcription	HMEC	breast
29	chr5:74779000-74786600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:74779000-74804200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:74782000-74786800	Weak transcription	Fetal Kidney	kidney
32	chr5:74782200-74795400	Weak transcription	HSMM	muscle
33	chr5:74782600-74805400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:74783000-74803000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:74783400-74787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:74783600-74793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:74784000-74787400	Weak transcription	HepG2	liver
38	chr5:74784000-74795400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:74784000-74803200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:74784200-74786600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:74785200-74786200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr5:74785200-74787200	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:74785200-74792600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:74785200-74803800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:74785400-74786200	ZNF genes & repeats	Primary T cells from cord blood	blood
46	chr5:74785400-74787200	Weak transcription	Fetal Intestine Large	intestine
47	chr5:74785400-74787400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:74785400-74794400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:74785400-74799000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:74785600-74786200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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