Variant report

Variant	rs4440336
Chromosome Location	chr5:74764347-74764348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10038723	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10043621	0.89[ASN][1000 genomes]
rs10044053	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10060260	0.83[EUR][1000 genomes]
rs10067641	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10070207	0.83[EUR][1000 genomes]
rs10075139	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10434644	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10462517	0.90[ASN][1000 genomes]
rs10474433	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs10474436	0.97[EUR][1000 genomes];0.95[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];0.87[ASN][1000 genomes]
rs10942739	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11957913	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12234032	0.85[ASN][1000 genomes]
rs13354407	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1427924	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17739580	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1863934	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1863935	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1995267	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[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];0.88[ASN][1000 genomes]
rs253392	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs253393	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs253407	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs253409	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs28609217	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2878519	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2878520	0.86[EUR][1000 genomes];0.86[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];0.88[ASN][1000 genomes]
rs34340	0.81[ASN][1000 genomes]
rs3761742	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs3761743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846665	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs3846666	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3931914	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4045166	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4385188	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703670	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4703674	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4704214	0.90[ASN][1000 genomes]
rs4704224	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704228	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57149337	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57312935	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744533	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5744555	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744575	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5744595	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5744598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5744601	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5744621	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5744663	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744703	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59506842	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61430233	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6453134	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67969809	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6861279	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6863398	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6872314	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6874781	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6886841	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6891949	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs698912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs73120833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7356637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7445415	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs767676	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7700468	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7701925	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs7706857	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7709282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7717505	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7723531	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7737959	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs924452	0.85[EUR][1000 genomes];0.85[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];0.85[ASN][1000 genomes]
rs9885386	0.89[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4440336	COL4A3BP	cis	cerebellum	SCAN
rs4440336	S100Z	cis	parietal	SCAN
rs4440336	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:66 , 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	chr5:74743000-74764400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:74748600-74770400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:74751600-74769000	Weak transcription	Liver	Liver
6	chr5:74758400-74764600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:74760400-74776800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:74760400-74792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:74761400-74764400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:74761600-74764400	Weak transcription	Esophagus	oesophagus
11	chr5:74762200-74764400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:74762200-74805800	Weak transcription	Pancreas	Pancrea
13	chr5:74762400-74764400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:74762400-74764600	Weak transcription	Fetal Heart	heart
15	chr5:74762600-74768600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:74762600-74770200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:74762600-74770800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:74762600-74778000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:74762800-74764400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:74762800-74770200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:74762800-74771000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:74763200-74769000	Weak transcription	Stomach Mucosa	stomach
23	chr5:74763200-74787400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:74763400-74764600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr5:74763600-74766800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:74763800-74766800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr5:74763800-74767200	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr5:74763800-74767200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:74764000-74764400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
30	chr5:74764000-74764600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr5:74764000-74764600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:74764000-74764600	ZNF genes & repeats	Fetal Kidney	kidney
33	chr5:74764000-74764800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:74764000-74764800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr5:74764000-74764800	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr5:74764000-74764800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
37	chr5:74764000-74765000	ZNF genes & repeats	Brain Anterior Caudate	brain
38	chr5:74764000-74765000	ZNF genes & repeats	Fetal Lung	lung
39	chr5:74764000-74765200	ZNF genes & repeats	GM12878-XiMat	blood
40	chr5:74764000-74766200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:74764000-74766600	ZNF genes & repeats	Dnd41	blood
42	chr5:74764000-74767200	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr5:74764200-74764600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:74764200-74764600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
45	chr5:74764200-74764600	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr5:74764200-74764600	ZNF genes & repeats	Fetal Stomach	stomach
47	chr5:74764200-74764600	Enhancers	Gastric	stomach
48	chr5:74764200-74764600	ZNF genes & repeats	Lung	lung
49	chr5:74764200-74764600	ZNF genes & repeats	Psoas Muscle	Psoas
50	chr5:74764200-74764800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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