Variant report

Variant	rs10911480
Chromosome Location	chr1:183954382-183954383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:183954011..183955861-chr1:184020180..184021943,2	K562	blood:
2	chr1:183950977..183955895-chr1:183999343..184002420,4	K562	blood:
3	chr1:183952222..183954901-chr1:183961001..183962966,2	K562	blood:

Variant related genes	Relation type
ENSG00000198860	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10752927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797925	0.99[ASN][1000 genomes]
rs10797926	0.99[ASN][1000 genomes]
rs10797927	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797929	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10797930	0.85[ASN][1000 genomes]
rs10797932	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10911477	0.99[ASN][1000 genomes]
rs10911481	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911483	0.99[ASN][1000 genomes]
rs10911484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10911485	0.85[ASN][1000 genomes]
rs10911486	0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12021841	1.00[CHB][hapmap];0.99[ASN][1000 genomes]
rs12023778	0.99[ASN][1000 genomes]
rs12027096	0.85[ASN][1000 genomes]
rs12028482	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030903	0.85[ASN][1000 genomes]
rs12030924	0.85[ASN][1000 genomes]
rs12034897	0.85[ASN][1000 genomes]
rs12034962	0.85[ASN][1000 genomes]
rs12042354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12059407	0.97[ASN][1000 genomes]
rs12060999	0.97[ASN][1000 genomes]
rs12061041	0.97[ASN][1000 genomes]
rs12064779	0.85[ASN][1000 genomes]
rs12069197	0.85[ASN][1000 genomes]
rs12085344	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1475402	0.85[ASN][1000 genomes]
rs16861859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1887282	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1887283	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1926866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1926868	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs1998926	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2025807	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2148672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148678	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2182623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662690	0.96[ASN][1000 genomes]
rs6698329	0.97[ASN][1000 genomes]
rs6701930	0.85[ASN][1000 genomes]
rs7410829	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs751410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832026	chr1:183785065-183961847	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533206	chr1:183861204-184091272	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10911480	RGSL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:183902600-183965200	Weak transcription	Left Ventricle	heart
2	chr1:183923200-183961000	Weak transcription	Pancreas	Pancrea
3	chr1:183950800-183954800	Weak transcription	Right Atrium	heart
4	chr1:183951400-183955000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:183952000-183958800	Enhancers	NHDF-Ad	bronchial
6	chr1:183952400-183955200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:183952800-183954400	Enhancers	Brain Substantia Nigra	brain
8	chr1:183953000-183959000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:183953000-183965200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:183953200-183957400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:183953600-183957600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:183953800-183954800	Weak transcription	K562	blood
13	chr1:183953800-183956600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:183953800-183965200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:183954000-183954600	Weak transcription	Lung	lung
16	chr1:183954000-183956000	Weak transcription	Fetal Heart	heart
17	chr1:183954000-183956400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:183954000-183958400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:183954000-183965600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:183954200-183955000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:183954200-183955200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:183954200-183956000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:183954200-183956000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:183954200-183956000	Weak transcription	NHLF	lung
25	chr1:183954200-183956400	Weak transcription	Brain Hippocampus Middle	brain

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