Variant report

Variant	rs12533673
Chromosome Location	chr7:39503427-39503428
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:37)

rs_ID	r²[population]
rs10233706	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10261375	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12111665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12112344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17171576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17171578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17713095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17713107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17713143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17769981	0.98[ASN][1000 genomes]
rs17769987	0.98[ASN][1000 genomes]
rs2024104	0.94[EUR][1000 genomes]
rs2052017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2073545	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2108717	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2237384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237386	0.87[ASN][1000 genomes]
rs2237387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237392	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2237397	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2237398	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2282915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299134	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3800850	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3819416	0.84[ASN][1000 genomes]
rs4720324	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4723864	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4723865	0.88[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6960142	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73388309	0.87[ASN][1000 genomes]
rs73388311	0.87[ASN][1000 genomes]
rs763894	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs885689	0.88[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][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	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv966782	chr7:39454992-39581886	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv1797871	chr7:39499852-39503496	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12533673	C7orf36	cis	parietal	SCAN
rs12533673	C7orf11	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39492000-39504800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:39497200-39503600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:39498200-39504600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:39499200-39504800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:39499400-39504400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:39499600-39504400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:39500600-39504800	Weak transcription	Fetal Brain Male	brain
8	chr7:39500800-39504000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:39500800-39504800	Weak transcription	K562	blood
10	chr7:39501200-39504800	Weak transcription	Dnd41	blood
11	chr7:39501800-39504800	Weak transcription	Fetal Kidney	kidney
12	chr7:39502200-39503600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:39502400-39504000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:39502400-39504800	Weak transcription	Fetal Lung	lung
15	chr7:39502600-39504000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:39502600-39508000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:39502800-39504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:39502800-39504800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:39502800-39504800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:39503000-39504200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:39503000-39504800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:39503400-39503800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:39503400-39504600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr7:39503400-39505400	Enhancers	Primary hematopoietic stem cells	blood

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