Variant report

Variant	rs2297088
Chromosome Location	chr9:98242984-98242985
allele	A/G
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	MAFF	chr9:98242970-98243029	K562	blood:	n/a	n/a
2	MAFK	chr9:98242973-98243259	HepG2	liver:	n/a	chr9:98243120-98243134

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98241516..98243611-chr9:98244641..98247119,2	K562	blood:
2	chr9:98239525..98243679-chr9:98243925..98247581,3	K562	blood:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10512248	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1355619	0.83[ASN][1000 genomes]
rs1355620	0.83[ASN][1000 genomes]
rs16909919	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066829	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236406	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236407	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274692	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2282042	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297086	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28457763	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28495472	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28496034	0.81[ASN][1000 genomes]
rs28504650	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28536201	0.83[ASN][1000 genomes]
rs28557305	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28620532	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28620668	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28629854	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28701981	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3758302	0.83[ASN][1000 genomes]
rs4448343	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
4	chr9:98226000-98251000	Weak transcription	Osteobl	bone
5	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
9	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
12	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
16	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:98233400-98243400	Strong transcription	Fetal Lung	lung
21	chr9:98233800-98243400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:98234200-98243000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:98234200-98243000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:98234400-98243000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:98234400-98243000	Strong transcription	Aorta	Aorta
26	chr9:98234400-98243000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:98237400-98243600	Strong transcription	HepG2	liver
28	chr9:98238200-98246400	Weak transcription	Psoas Muscle	Psoas
29	chr9:98239400-98247200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:98239400-98251400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:98239600-98253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:98239800-98243800	Strong transcription	HSMM	muscle
33	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:98240000-98243000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:98240000-98247600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr9:98240200-98243600	Enhancers	Brain Germinal Matrix	brain
37	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:98240400-98243800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr9:98240400-98246400	Weak transcription	Right Ventricle	heart
40	chr9:98240400-98256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:98240600-98243400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:98240600-98245000	Enhancers	Brain Substantia Nigra	brain
43	chr9:98240800-98243000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:98240800-98243000	Genic enhancers	Ovary	ovary
45	chr9:98240800-98243200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:98241000-98243000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr9:98241000-98243400	Weak transcription	Primary T cells from cord blood	blood
49	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:98241200-98248800	Weak transcription	Colonic Mucosa	Colon

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