Variant report

Variant	rs678640
Chromosome Location	chr1:212719366-212719367
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	chr1:212719262..212723059-chr1:212724838..212729045,5	K562	blood:
2	chr1:212719347..212721622-chr1:212726171..212729045,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10779581	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863978	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863979	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10863980	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10863981	0.86[JPT][hapmap]
rs11119951	0.83[GIH][hapmap]
rs11119953	0.83[GIH][hapmap]
rs11119956	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11119957	0.95[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119962	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119963	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119965	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119970	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119972	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs11119973	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs11119974	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11119975	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11119977	0.85[JPT][hapmap]
rs12038766	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12041940	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12136405	0.83[AMR][1000 genomes]
rs12410743	0.83[ASN][1000 genomes]
rs12568048	0.83[GIH][hapmap]
rs12729140	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1331059	1.00[YRI][hapmap]
rs3806460	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4347269	0.83[ASN][1000 genomes]
rs4951453	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951606	0.90[CHB][hapmap]
rs4951609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951613	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs502502	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs510189	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs580570	1.00[YRI][hapmap]
rs587293	0.81[ASN][1000 genomes]
rs606996	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs613477	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs616408	0.80[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs634906	1.00[YRI][hapmap]
rs644143	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs665435	1.00[YRI][hapmap]
rs72649991	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72649993	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553505	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs791561	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs791852	0.86[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs678640	LQK1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212714000-212722600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212717000-212721600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:212718200-212720200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:212718600-212720000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:212718600-212720400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:212718600-212720400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:212718600-212720400	Enhancers	Brain Hippocampus Middle	brain
8	chr1:212718600-212731400	Weak transcription	Right Atrium	heart
9	chr1:212719000-212719600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:212719000-212719800	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:212719000-212719800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:212719000-212719800	Enhancers	Fetal Intestine Large	intestine
13	chr1:212719000-212719800	Enhancers	Placenta	Placenta
14	chr1:212719000-212719800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:212719000-212720000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:212719000-212720000	Enhancers	Brain Anterior Caudate	brain
17	chr1:212719000-212720200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:212719000-212720400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:212719000-212720600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:212719000-212720600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:212719000-212720600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:212719200-212720000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:212719200-212720000	Enhancers	Brain Angular Gyrus	brain
24	chr1:212719200-212720000	Enhancers	Brain Substantia Nigra	brain
25	chr1:212719200-212720800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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