Variant report

Variant	rs4742708
Chromosome Location	chr9:100721018-100721019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100720511..100723623-chr9:100818470..100820137,3	K562	blood:
2	chr9:100716917..100718589-chr9:100720571..100722147,3	K562	blood:
3	chr9:100681341..100688036-chr9:100719041..100726043,8	K562	blood:
4	chr9:100713086..100729092-chr9:100738274..100752806,69	K562	blood:
5	chr9:100703047..100707338-chr9:100720648..100725664,5	K562	blood:
6	chr9:100716666..100719267-chr9:100720012..100722937,7	K562	blood:
7	chr9:100698423..100701037-chr9:100720373..100724214,5	K562	blood:
8	chr9:100681285..100688110-chr9:100720096..100725626,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000136929	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10512256	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059003	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984009	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs10984098	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10984377	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984516	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984522	0.92[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984532	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984545	0.86[CEU][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156487	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375612	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376113	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1348387	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443433	0.82[GIH][hapmap]
rs17687621	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1947015	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514106	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4743143	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743144	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743149	0.93[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55978521	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037172	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043516	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs72753537	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72753557	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753579	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753581	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753588	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851498	0.87[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854948	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4742708	GALNT12	cis	lymphoblastoid	seeQTL
rs4742708	C9orf156	cis	cerebellum	SCAN
rs4742708	ZNF782	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100713600-100724200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr9:100720600-100722600	Enhancers	K562	blood
3	chr9:100721000-100721400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:100721000-100721600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:100721000-100721600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:100721000-100721600	Enhancers	HSMM	muscle
7	chr9:100721000-100721800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:100721000-100721800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr9:100721000-100721800	Enhancers	Brain Anterior Caudate	brain
10	chr9:100721000-100721800	Enhancers	HSMMtube	muscle
11	chr9:100721000-100721800	Enhancers	NHLF	lung
12	chr9:100721000-100722000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:100721000-100722000	Enhancers	Brain Hippocampus Middle	brain
14	chr9:100721000-100722000	Enhancers	Osteobl	bone
15	chr9:100721000-100722200	Enhancers	Brain Angular Gyrus	brain
16	chr9:100721000-100722400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:100721000-100722400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:100721000-100722400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:100721000-100722400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr9:100721000-100722400	Enhancers	Brain Substantia Nigra	brain
21	chr9:100721000-100722600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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