Variant report

Variant	rs10070207
Chromosome Location	chr5:74745228-74745229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10075139	0.80[ASN][1000 genomes]
rs10434644	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10474436	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1051795	0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs10942739	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2287711	0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs253407	0.80[JPT][hapmap]
rs253409	0.80[JPT][hapmap]
rs3213801	0.81[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs3761742	0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs3761743	0.90[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs3846665	0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs3931914	0.85[JPT][hapmap]
rs4045166	0.90[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs4385188	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4440336	0.83[EUR][1000 genomes]
rs4703670	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4703674	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap]
rs57149337	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5744533	0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs5744555	0.90[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.80[ASN][1000 genomes]
rs5744598	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs5744601	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6453134	0.81[EUR][1000 genomes]
rs6861279	0.85[CHB][hapmap]
rs6863398	0.80[ASN][1000 genomes]
rs6872314	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6891949	0.81[EUR][1000 genomes]
rs698912	0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs7356637	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs767676	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7700468	0.90[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs7701925	0.85[JPT][hapmap]
rs7709282	0.90[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs7717505	0.85[CHB][hapmap]
rs9332464	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10070207	COL4A3BP	cis	cerebellum	SCAN
rs10070207	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
2	chr5:74706200-74756400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:74708400-74746000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:74709600-74760200	Weak transcription	Gastric	stomach
5	chr5:74713200-74753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:74721800-74749600	Weak transcription	Adipose Nuclei	Adipose
7	chr5:74722200-74749800	Weak transcription	Liver	Liver
8	chr5:74730400-74757400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:74731800-74757400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:74732000-74756800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:74732000-74760200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:74732000-74787400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:74737600-74749800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:74738600-74756600	Weak transcription	Fetal Kidney	kidney
15	chr5:74739600-74756200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:74740000-74761600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:74741200-74746800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:74741200-74760200	Weak transcription	Left Ventricle	heart
19	chr5:74742400-74749200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:74742400-74794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:74742600-74745600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:74742600-74764200	Weak transcription	HSMM	muscle
23	chr5:74743000-74746000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:74743000-74746000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:74743000-74749400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:74743000-74749800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:74743000-74749800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:74743000-74750000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:74743000-74750200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:74743000-74752600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:74743000-74754800	Weak transcription	Fetal Lung	lung
32	chr5:74743000-74757000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:74743000-74760000	Weak transcription	Lung	lung
34	chr5:74743000-74761400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:74743000-74761600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:74743000-74763400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:74743000-74764400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:74743200-74745800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:74743200-74746000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr5:74743200-74746000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:74743200-74747000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:74743200-74749600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr5:74743200-74749600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:74743200-74749600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:74743200-74749800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:74743200-74749800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr5:74743200-74750400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:74743200-74752600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr5:74743200-74753600	Weak transcription	Dnd41	blood
50	chr5:74743200-74754800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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