Variant report

Variant	rs10408461
Chromosome Location	chr19:44330772-44330773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:44330749-44332187	A549	lung:	n/a	chr19:44331687-44331697

No.	Distal block	Cell Line	Cell type
1	chr19:44330249..44332710-chr19:44437495..44440338,2	MCF-7	breast:
2	chr19:44330466..44332260-chr19:44438054..44440025,2	K562	blood:
3	chr19:44257672..44259708-chr19:44329404..44331468,2	K562	blood:
4	chr19:44323198..44325701-chr19:44330167..44332994,2	K562	blood:

Variant related genes	Relation type
ZNF283	TF binding region
ENSG00000124459	Chromatin interaction
ENSG00000159871	Chromatin interaction
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036246	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10405318	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10412955	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10415344	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10416116	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10421861	0.86[GIH][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs10500286	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10500287	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11878787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462507	0.94[ASN][1000 genomes]
rs12608578	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13344589	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549953	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549954	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549955	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549956	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549957	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549959	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565057	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17712224	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1909	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1964381	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994414	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1994415	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1994416	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2016345	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2099356	0.94[ASN][1000 genomes]
rs2163855	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2195981	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2217669	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2356401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2356403	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2356432	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2356433	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2356434	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2356438	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2356439	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239948	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239949	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2883946	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap]
rs349032	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4511643	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57096959	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57133938	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59503823	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60036744	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60085895	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62114569	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62118368	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62118369	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62118371	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62118372	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509120	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7247308	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247863	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7248807	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7253002	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253606	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254659	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7259647	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73052639	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73052665	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7508701	0.96[ASN][1000 genomes]
rs8099861	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106802	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8112065	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8113286	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10408461	CD3EAP	cis	cerebellum	SCAN
rs10408461	ZNF404	trans	parietal	SCAN
rs10408461	PRKD2	cis	parietal	SCAN
rs10408461	TBC1D17	cis	parietal	SCAN
rs10408461	DMPK	cis	cerebellum	SCAN
rs10408461	IZUMO2	cis	cerebellum	SCAN
rs10408461	KLK8	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44325000-44331000	Weak transcription	Aorta	Aorta
2	chr19:44325000-44331000	Weak transcription	Spleen	Spleen
3	chr19:44325200-44330800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:44325200-44330800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:44325200-44330800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr19:44325200-44330800	Weak transcription	NHEK	skin
7	chr19:44325200-44331000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:44325400-44330800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:44325400-44330800	Weak transcription	Brain Hippocampus Middle	brain
10	chr19:44325400-44330800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:44325400-44331000	Weak transcription	HMEC	breast
12	chr19:44330200-44331000	Enhancers	Lung	lung
13	chr19:44330200-44331000	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr19:44330400-44332000	Active TSS	Fetal Brain Female	brain
15	chr19:44330600-44330800	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:44330600-44330800	Enhancers	Brain Angular Gyrus	brain
17	chr19:44330600-44330800	Weak transcription	Brain Anterior Caudate	brain
18	chr19:44330600-44330800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr19:44330600-44330800	Bivalent Enhancer	Fetal Brain Male	brain
20	chr19:44330600-44330800	Active TSS	Thymus	Thymus
21	chr19:44330600-44332200	Active TSS	Pancreatic Islets	Pancreatic Islet

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