Variant report

Variant	rs2805832
Chromosome Location	chr9:100462880-100462881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:100462766-100463025	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100457791..100462084-chr9:100462112..100466505,5	K562	blood:
2	chr9:100461133..100463354-chr9:100744707..100746870,2	MCF-7	breast:

Variant related genes	Relation type
XPA	TF binding region
ENSG00000214417	Chromatin interaction
ENSG00000136936	Chromatin interaction
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10983030	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983447	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12379552	0.83[EUR][1000 genomes]
rs1800975	0.82[ASW][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026132	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2036959	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2668792	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2668793	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2668798	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2773347	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2773351	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2805767	0.88[EUR][1000 genomes]
rs2805775	0.87[EUR][1000 genomes]
rs2805777	0.86[EUR][1000 genomes]
rs2805779	0.86[EUR][1000 genomes]
rs2805824	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2805825	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2805826	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2805828	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2805829	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2805837	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2805839	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2805840	0.87[EUR][1000 genomes]
rs2808668	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2808673	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2808675	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2808677	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2808683	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2808685	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808686	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808687	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2808689	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2808691	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2808692	0.89[EUR][1000 genomes]
rs2808701	0.87[EUR][1000 genomes]
rs2808703	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6478325	0.87[EUR][1000 genomes]
rs7853179	0.84[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	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv972792	chr9:100460351-100466365	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100459800-100466400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:100460000-100465400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:100460200-100465400	Weak transcription	HSMM	muscle
4	chr9:100460400-100465000	Weak transcription	Fetal Intestine Small	intestine
5	chr9:100460400-100465200	Weak transcription	Liver	Liver
6	chr9:100460400-100465200	Weak transcription	Hela-S3	cervix
7	chr9:100460400-100465400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:100460400-100465400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:100460400-100465400	Weak transcription	Fetal Intestine Large	intestine
10	chr9:100460400-100465400	Weak transcription	HSMMtube	muscle
11	chr9:100460400-100465600	Weak transcription	Pancreas	Pancrea
12	chr9:100460400-100465600	Weak transcription	HUVEC	blood vessel
13	chr9:100460400-100465800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:100460400-100465800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:100460400-100465800	Weak transcription	Stomach Mucosa	stomach
16	chr9:100460400-100467000	Weak transcription	Esophagus	oesophagus
17	chr9:100460400-100467800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:100460600-100465000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:100460600-100465200	Weak transcription	Fetal Kidney	kidney
20	chr9:100460600-100465200	Weak transcription	A549	lung
21	chr9:100461400-100467800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr9:100461600-100465400	Weak transcription	HMEC	breast
23	chr9:100461600-100467200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:100462200-100466000	Weak transcription	K562	blood
25	chr9:100462400-100465200	Weak transcription	GM12878-XiMat	blood
26	chr9:100462400-100472800	Weak transcription	Brain Substantia Nigra	brain
27	chr9:100462600-100463200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:100462800-100463200	Weak transcription	HepG2	liver

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