Variant report

Variant	rs6898923
Chromosome Location	chr5:178330559-178330560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10035887	1.00[ASN][1000 genomes]
rs10043579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044051	0.99[ASN][1000 genomes]
rs10055777	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10055826	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10071186	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10434800	0.86[ASN][1000 genomes]
rs10516151	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11249601	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11249603	0.97[ASN][1000 genomes]
rs11745403	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11746382	0.97[ASN][1000 genomes]
rs12653764	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13154558	0.98[ASN][1000 genomes]
rs13362387	0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1496949	0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1496950	0.99[ASN][1000 genomes]
rs1995079	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2004503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4444956	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs4700927	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6600993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600994	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866021	0.99[ASN][1000 genomes]
rs6872605	0.98[ASN][1000 genomes]
rs6872794	0.98[ASN][1000 genomes]
rs6873993	0.98[ASN][1000 genomes]
rs6880072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6897783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7701607	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7702879	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7718717	0.86[ASN][1000 genomes]
rs953740	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6898923	TMED9	cis	parietal	SCAN
rs6898923	N4BP3	cis	parietal	SCAN
rs6898923	BTNL9	cis	cerebellum	SCAN
rs6898923	HNRNPAB	cis	parietal	SCAN
rs6898923	ZFP2	cis	cerebellum	SCAN
rs6898923	ZNF454	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178323600-178331200	Weak transcription	Pancreas	Pancrea
2	chr5:178323600-178332800	Weak transcription	Left Ventricle	heart
3	chr5:178323600-178335400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:178323800-178331000	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:178323800-178332800	Weak transcription	Placenta	Placenta
6	chr5:178323800-178332800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:178323800-178333800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:178323800-178336200	Weak transcription	Right Ventricle	heart
9	chr5:178323800-178336400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:178324000-178332800	Weak transcription	Brain Angular Gyrus	brain
11	chr5:178324000-178332800	Weak transcription	Brain Anterior Caudate	brain
12	chr5:178325800-178332800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:178328000-178334400	Weak transcription	Psoas Muscle	Psoas
14	chr5:178328600-178331200	Weak transcription	Aorta	Aorta
15	chr5:178328600-178332800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:178328600-178332800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:178328600-178332800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:178328600-178332800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:178328600-178332800	Weak transcription	Gastric	stomach
20	chr5:178328800-178332800	Weak transcription	Ovary	ovary
21	chr5:178329600-178332800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:178330200-178331000	Weak transcription	Liver	Liver
23	chr5:178330200-178332800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:178330400-178331200	Weak transcription	Fetal Lung	lung

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