Variant report

Variant	rs1028355
Chromosome Location	chr6:163788191-163788192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163788145..163792575-chr6:163834513..163836469,4	K562	blood:
2	chr6:163770647..163772827-chr6:163787676..163789505,2	K562	blood:
3	chr6:163787459..163789359-chr6:163790484..163793224,2	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1028354	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13204618	0.89[ASN][1000 genomes]
rs13220178	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1336227	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1541142	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541143	0.98[ASN][1000 genomes]
rs1628413	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1737310	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1737312	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1737313	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1737315	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1764000	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1764001	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1764003	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1764005	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1764006	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2473220	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2784870	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35570774	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4708994	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]
rs760890	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9365559	0.81[AMR][1000 genomes]
rs9365562	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs945534	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1028355	QKI	cis	parietal	SCAN
rs1028355	IGF2R	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163777400-163790000	Weak transcription	Spleen	Spleen
2	chr6:163777400-163791400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:163778000-163788600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:163778400-163790800	Weak transcription	Right Atrium	heart
5	chr6:163783800-163791800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:163784000-163789600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:163784000-163791000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:163784200-163790000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:163784400-163788600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:163786800-163788200	Enhancers	Brain Substantia Nigra	brain
11	chr6:163787400-163789200	Enhancers	Brain Hippocampus Middle	brain
12	chr6:163787600-163791800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:163788000-163788200	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:163788000-163789000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:163788000-163789000	Enhancers	Adipose Nuclei	Adipose
16	chr6:163788000-163791000	Weak transcription	Brain Cingulate Gyrus	brain

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