Variant report

Variant	rs9472701
Chromosome Location	chr6:46116449-46116450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:46112224..46114185-chr6:46116270..46118117,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1011370	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1047153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1048076	0.80[GIH][hapmap]
rs1048077	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs1076738	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs13210417	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2143747	0.82[GIH][hapmap]
rs2179760	0.82[GIH][hapmap]
rs3734208	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4496799	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714902	0.84[CEU][hapmap]
rs5011271	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6458491	0.82[GIH][hapmap]
rs6900403	0.91[ASN][1000 genomes]
rs6921636	0.89[ASN][1000 genomes]
rs7357078	0.80[GIH][hapmap]
rs7754915	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs7760042	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7762549	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7766019	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7772635	0.87[EUR][1000 genomes]
rs7775082	0.82[GIH][hapmap]
rs9367235	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369597	0.96[CEU][hapmap]
rs9369598	0.85[ASN][1000 genomes]
rs9395154	0.85[ASN][1000 genomes]
rs9395156	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472686	0.85[ASN][1000 genomes]
rs9472703	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472712	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs993632	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs995563	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs995564	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022912	chr6:46093409-46116449	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	esv1842212	chr6:46111940-46127836	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9472701	CLIC5	cis	parietal	SCAN
rs9472701	RHAG	cis	cerebellum	SCAN
rs9472701	ENPP4	cis	parietal	SCAN
rs9472701	ENPP5	cis	brain	seeQTL
rs9472701	ZNF318	cis	parietal	SCAN
rs9472701	CRISP3	cis	parietal	SCAN
rs9472701	ENPP5	cis	cerebellum	SCAN
rs9472701	ENPP5	cis	parietal	SCAN
rs9472701	PPP2R5D	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46098800-46117800	Weak transcription	Gastric	stomach
2	chr6:46098800-46129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:46105400-46133800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:46105600-46128600	Weak transcription	Brain Angular Gyrus	brain
5	chr6:46105600-46137400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:46106400-46125400	Weak transcription	Psoas Muscle	Psoas
7	chr6:46106400-46138000	Weak transcription	Lung	lung
8	chr6:46108000-46130000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:46111400-46117200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:46111400-46125200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:46111400-46128600	Weak transcription	Primary T cells from cord blood	blood
12	chr6:46111400-46128800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:46111400-46137800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:46111600-46116600	Weak transcription	Primary B cells from cord blood	blood
15	chr6:46111600-46116600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:46111600-46138000	Weak transcription	Fetal Thymus	thymus
17	chr6:46114000-46125600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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