Variant report

Variant	rs6660011
Chromosome Location	chr1:171827523-171827524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171816904..171819666-chr1:171826031..171827710,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015008	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1022541	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1040517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737337	0.86[ASN][1000 genomes]
rs10737338	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753203	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753205	0.85[ASN][1000 genomes]
rs1076700	0.85[ASN][1000 genomes]
rs10798695	0.85[ASN][1000 genomes]
rs10798701	0.85[ASN][1000 genomes]
rs10798702	0.85[ASN][1000 genomes]
rs10798705	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798706	0.84[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs10798716	0.85[ASN][1000 genomes]
rs10798722	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798725	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913908	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1118173	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs12021814	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12024869	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs12025243	0.86[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap]
rs12029015	0.81[EUR][1000 genomes]
rs12040254	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12047542	0.82[EUR][1000 genomes]
rs12239702	0.81[ASN][1000 genomes]
rs12405583	0.85[ASN][1000 genomes]
rs12747663	0.82[EUR][1000 genomes]
rs1535301	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1972340	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980488	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145383	0.86[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2206543	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs2235696	0.85[ASN][1000 genomes]
rs2421915	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs2421947	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs2901600	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs34906981	0.89[EUR][1000 genomes]
rs4500358	0.85[ASN][1000 genomes]
rs4596936	0.89[EUR][1000 genomes]
rs4916235	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916400	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916401	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916402	0.85[ASN][1000 genomes]
rs4916403	0.85[ASN][1000 genomes]
rs4916404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916411	0.89[EUR][1000 genomes]
rs6425454	0.85[ASN][1000 genomes]
rs6425455	0.85[ASN][1000 genomes]
rs6425456	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425468	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425484	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6425518	0.81[EUR][1000 genomes]
rs6657315	0.85[ASN][1000 genomes]
rs6665335	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679341	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683945	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs6685974	0.85[ASN][1000 genomes]
rs6686260	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6689231	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs6690848	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6701033	0.85[CHD][hapmap]
rs6702944	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs71523161	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs742509	0.85[ASN][1000 genomes]
rs742510	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7514627	0.85[ASN][1000 genomes]
rs7517331	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7554700	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7554935	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926545	0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs926546	0.84[ASN][1000 genomes]
rs965051	0.84[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6660011	NME7	cis	parietal	SCAN
rs6660011	KIFAP3	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171812200-171833200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:171814600-171833400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:171819600-171832800	Weak transcription	Left Ventricle	heart
4	chr1:171820200-171832600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:171820600-171827600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:171821800-171829600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:171822200-171832800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:171822400-171827600	Weak transcription	NHDF-Ad	bronchial
9	chr1:171822400-171828000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:171822400-171832200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:171825800-171832800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:171826600-171829800	Weak transcription	Ovary	ovary
13	chr1:171827200-171832800	Weak transcription	Brain Substantia Nigra	brain

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