Variant report

Variant	rs7700468
Chromosome Location	chr5:74675076-74675077
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	chr5:74674905..74677858-chr5:74706669..74708493,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10038723	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10043621	0.80[ASN][1000 genomes]
rs10053643	0.87[ASN][1000 genomes]
rs10075139	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10434644	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10462517	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10473972	0.87[ASN][1000 genomes]
rs10474433	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs10474434	0.87[ASN][1000 genomes]
rs10474436	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10942739	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11957913	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12234032	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13354407	0.80[ASN][1000 genomes]
rs17238484	0.87[ASN][1000 genomes]
rs1995267	0.85[EUR][1000 genomes]
rs28609217	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2878418	0.83[ASN][1000 genomes]
rs3761742	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846665	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846666	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3931914	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4385188	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4440336	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703670	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4703674	0.83[EUR][1000 genomes]
rs4704214	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704224	0.91[EUR][1000 genomes]
rs57149337	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744533	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs5744555	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs5744575	0.81[ASN][1000 genomes]
rs5744595	0.85[EUR][1000 genomes]
rs5744598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5744601	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5744621	0.80[ASN][1000 genomes]
rs5744663	0.82[EUR][1000 genomes]
rs5744703	0.85[EUR][1000 genomes]
rs61430233	0.89[ASN][1000 genomes]
rs6453133	0.89[AFR][1000 genomes]
rs6453134	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6863398	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6872314	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6874781	0.84[ASN][1000 genomes]
rs6891949	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs698912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120833	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7356637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7445415	0.81[ASN][1000 genomes]
rs767676	0.85[EUR][1000 genomes]
rs7701925	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7709282	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];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7732854	0.80[ASN][1000 genomes]
rs7737959	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885386	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7700468	S100Z	cis	parietal	SCAN
rs7700468	COL4A3BP	cis	cerebellum	SCAN
rs7700468	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74676800	Weak transcription	Fetal Brain Male	brain
2	chr5:74656400-74687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:74656600-74675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:74656600-74675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:74656600-74675800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:74656600-74676800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:74656600-74677200	Weak transcription	Aorta	Aorta
9	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
10	chr5:74656800-74676200	Weak transcription	Colonic Mucosa	Colon
11	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:74659600-74675800	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:74659800-74677000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:74659800-74684800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
18	chr5:74660200-74707800	Weak transcription	Stomach Mucosa	stomach
19	chr5:74661800-74683600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:74663200-74676800	Weak transcription	K562	blood
21	chr5:74664600-74676800	Weak transcription	NHLF	lung
22	chr5:74664600-74677000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:74664800-74677000	Weak transcription	HUVEC	blood vessel
24	chr5:74665000-74703000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:74667200-74688200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:74667200-74693600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:74667600-74687600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:74668000-74688400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:74668200-74686200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:74668400-74685600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:74668600-74677200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:74668600-74677600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:74668600-74681600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:74668600-74686800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:74668600-74687200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:74668600-74687600	Strong transcription	Adipose Nuclei	Adipose
38	chr5:74668600-74687600	Strong transcription	Fetal Lung	lung
39	chr5:74668600-74691200	Strong transcription	Liver	Liver
40	chr5:74668800-74685800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr5:74669400-74678600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:74669600-74681400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr5:74670000-74676800	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:74670000-74678000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:74670800-74676000	Weak transcription	NHDF-Ad	bronchial
46	chr5:74670800-74709400	Weak transcription	Pancreas	Pancrea
47	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
48	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:74671000-74675200	Weak transcription	HSMMtube	muscle
50	chr5:74671000-74686000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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