Variant report

Variant	rs9354910
Chromosome Location	chr6:70968660-70968661
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	chr6:70954782..70956814-chr6:70966578..70968796,2	K562	blood:

Variant related genes	Relation type
ENSG00000112280	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10806630	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10806631	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10806632	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10945202	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10945205	0.95[ASN][1000 genomes]
rs10945206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10945209	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10945210	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11757395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12153874	0.84[ASN][1000 genomes]
rs12153902	0.91[ASN][1000 genomes]
rs12154117	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs12189655	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12191701	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12191702	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12192237	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs12193867	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12195310	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12195966	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12195968	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12196905	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12201626	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs12204438	1.00[JPT][hapmap]
rs12205998	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12209857	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12210719	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs12210870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211880	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12213613	0.91[ASN][1000 genomes]
rs1321059	1.00[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1464159	0.82[ASN][1000 genomes]
rs1711729	0.96[ASN][1000 genomes]
rs17581483	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2176356	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2274584	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274586	0.88[EUR][1000 genomes]
rs45464198	0.95[ASN][1000 genomes]
rs510423	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55860958	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59322080	0.91[ASN][1000 genomes]
rs6922941	0.91[ASN][1000 genomes]
rs6923114	0.95[ASN][1000 genomes]
rs6932776	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs72923164	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72923166	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72924908	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7741471	0.83[ASN][1000 genomes]
rs7759110	0.91[ASN][1000 genomes]
rs9354911	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv886143	chr6:70968276-70984436	Strong transcription Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9354910	COL9A1	cis	cerebellum	SCAN
rs9354910	LMBRD1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70952200-70980400	Weak transcription	Fetal Stomach	stomach
2	chr6:70952200-70990000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:70952600-70980400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:70952800-70989800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:70955200-70971000	Weak transcription	Fetal Kidney	kidney
6	chr6:70962000-70983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:70965200-70991600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:70965400-70969200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:70968000-70968800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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