Variant report

Variant	rs13229007
Chromosome Location	chr7:11617445-11617446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10486153	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10486154	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs12112423	0.80[CEU][hapmap]
rs12112567	0.80[CEU][hapmap]
rs12699208	0.82[CEU][hapmap]
rs12699236	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12699241	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs12699242	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs12699243	0.94[CEU][hapmap];0.83[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12699244	0.94[CEU][hapmap];0.84[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12699245	0.94[CEU][hapmap];0.84[CHB][hapmap]
rs12699246	0.94[CEU][hapmap];0.89[CHB][hapmap]
rs12699247	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs12699248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13229378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229567	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246013	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17164823	0.94[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs2040816	0.88[CEU][hapmap];0.92[AMR][1000 genomes]
rs2040817	0.94[CEU][hapmap];0.87[AMR][1000 genomes]
rs2072139	0.80[CEU][hapmap]
rs2074605	0.82[CEU][hapmap]
rs2883564	0.82[CEU][hapmap]
rs6980325	0.83[ASN][1000 genomes]
rs764195	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7777369	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7790988	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs916988	0.83[AMR][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	nsv1028326	chr7:11221209-11754436	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv538733	chr7:11221209-11754436	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1023665	chr7:11457493-11773517	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv887606	chr7:11473561-11771288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11617000-11619200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr7:11617200-11617800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:11617200-11618000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:11617200-11619200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:11617400-11617600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:11617400-11617800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr7:11617400-11618000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr7:11617400-11618200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr7:11617400-11618400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:11617400-11618400	Weak transcription	Brain Germinal Matrix	brain

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