Variant report

Variant	rs6681171
Chromosome Location	chr1:212892113-212892114
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212891784..212893454-chr1:212900390..212902771,2	MCF-7	breast:
2	chr1:212838305..212839230-chr1:212892041..212892642,2	MCF-7	breast:
3	chr1:212890618..212893441-chr1:212895011..212896992,2	K562	blood:
4	chr1:212872500..212873127-chr1:212891520..212892244,2	MCF-7	breast:
5	chr1:212838311..212839215-chr1:212891572..212892116,2	K562	blood:

Variant related genes	Relation type
ENSG00000237980	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10127512	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10127703	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10127756	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1046083	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10465693	0.83[ASN][1000 genomes]
rs10863988	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10863989	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863997	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120001	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120006	0.83[ASN][1000 genomes]
rs11120007	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120010	0.81[ASN][1000 genomes]
rs11120014	0.81[ASN][1000 genomes]
rs11120017	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11120029	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs11120030	0.94[EUR][1000 genomes]
rs11556187	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11800642	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11806535	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11809232	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11809382	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11810895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811017	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12119531	1.00[ASN][1000 genomes]
rs12125867	0.83[ASN][1000 genomes]
rs12128410	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs12128903	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12129465	0.81[ASN][1000 genomes]
rs12133174	0.81[ASN][1000 genomes]
rs12137768	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12139618	1.00[ASN][1000 genomes]
rs12402370	0.86[ASN][1000 genomes]
rs12404618	0.81[ASN][1000 genomes]
rs12404885	0.81[ASN][1000 genomes]
rs12729663	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13376317	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13376383	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13376390	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1507357	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1507358	0.81[ASN][1000 genomes]
rs1532951	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs17019726	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs1857971	0.81[ASN][1000 genomes]
rs2135823	0.83[ASN][1000 genomes]
rs2174780	0.94[ASN][1000 genomes]
rs2174781	0.83[ASN][1000 genomes]
rs2271148	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2358899	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28872849	0.83[ASN][1000 genomes]
rs34110137	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35213366	0.92[EUR][1000 genomes]
rs3738803	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55840547	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56088044	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56243109	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57449384	0.86[ASN][1000 genomes]
rs59231663	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60308869	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540760	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540762	0.81[ASN][1000 genomes]
rs6662981	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664049	0.83[ASN][1000 genomes]
rs6665365	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6670648	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671866	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6687672	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6688238	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6694190	0.88[CEU][hapmap]
rs6694448	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700204	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6702101	0.83[ASN][1000 genomes]
rs73081830	0.83[ASN][1000 genomes]
rs73081853	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73081902	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73083707	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73083727	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73083731	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73083743	0.86[ASN][1000 genomes]
rs73083749	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73083756	0.94[EUR][1000 genomes]
rs73083765	0.94[EUR][1000 genomes]
rs7516312	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7519582	0.94[EUR][1000 genomes]
rs7525518	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527216	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536456	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7536629	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537598	0.83[ASN][1000 genomes]
rs7538755	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7546462	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546564	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546754	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7548861	0.94[EUR][1000 genomes]
rs7550288	0.83[ASN][1000 genomes]
rs7552880	0.95[EUR][1000 genomes];0.86[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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6681171	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212886400-212894400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:212886600-212894400	Weak transcription	Osteobl	bone
3	chr1:212891800-212892200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:212892000-212894600	Weak transcription	A549	lung
5	chr1:212892000-212894600	Weak transcription	NHDF-Ad	bronchial

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