Variant report

Variant	rs4708994
Chromosome Location	chr6:163779858-163779859
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1028354	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1028355	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13204618	0.84[ASN][1000 genomes]
rs13220178	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs1336227	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1541142	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1541143	0.86[ASN][1000 genomes]
rs1628413	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1737310	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1737312	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1737313	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1737315	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764000	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1764001	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1764003	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764005	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764006	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2473220	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2784870	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35570774	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs760890	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9365559	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9365562	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs945534	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4708994	QKI	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163776400-163783400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:163777400-163780000	Weak transcription	Right Ventricle	heart
3	chr6:163777400-163786800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:163777400-163787400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:163777400-163790000	Weak transcription	Spleen	Spleen
6	chr6:163777400-163791400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:163777600-163781400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:163778000-163788600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:163778400-163780200	Weak transcription	Brain Substantia Nigra	brain
10	chr6:163778400-163781400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:163778400-163781600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:163778400-163782000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:163778400-163783200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:163778400-163790800	Weak transcription	Right Atrium	heart
15	chr6:163778600-163780000	Weak transcription	Brain Angular Gyrus	brain
16	chr6:163778600-163782000	Weak transcription	Brain Anterior Caudate	brain
17	chr6:163778600-163783400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:163779400-163780200	Enhancers	Brain Hippocampus Middle	brain
19	chr6:163779400-163780400	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:163779400-163780400	Enhancers	Left Ventricle	heart
21	chr6:163779400-163780800	Enhancers	Fetal Muscle Leg	muscle
22	chr6:163779800-163780200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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