Variant report

Variant	rs2282042
Chromosome Location	chr9:98248635-98248636
allele	A/C
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	GATA3	chr9:98248336-98248959	T-47D	breast:	n/a	chr9:98248822-98248829
2	GATA3	chr9:98248351-98248687	MCF-7	breast:	n/a	n/a
3	FOXA1	chr9:98248374-98248851	T-47D	breast:	n/a	chr9:98248565-98248580
4	SIN3AK20	chr9:98248127-98249124	MCF-7	breast:	n/a	n/a
5	FOXA1	chr9:98248358-98248821	T-47D	breast:	n/a	chr9:98248565-98248580
6	GATA3	chr9:98248367-98248947	T-47D	breast:	n/a	chr9:98248822-98248829
7	GATA3	chr9:98248201-98249079	MCF-7	breast:	n/a	chr9:98248822-98248829 chr9:98248210-98248231
8	GATA3	chr9:98248445-98248969	MCF-7	breast:	n/a	chr9:98248822-98248829

No.	Distal block	Cell Line	Cell type
1	chr9:98239360..98245560-chr9:98246637..98251770,7	MCF-7	breast:
2	chr9:98248561..98250430-chr9:98258742..98261519,2	MCF-7	breast:
3	chr9:98146030..98146678-chr9:98247936..98248929,2	MCF-7	breast:
4	chr9:98247307..98248885-chr9:98260285..98262282,2	MCF-7	breast:
5	chr9:98246647..98248663-chr9:98399249..98402157,2	K562	blood:
6	chr9:98247877..98250406-chr9:98263082..98264686,2	K562	blood:
7	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
8	chr9:98248481..98249380-chr9:98261714..98262530,2	MCF-7	breast:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000185920	Chromatin interaction
ENSG00000271155	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10512248	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1355619	0.84[ASN][1000 genomes]
rs1355620	0.84[ASN][1000 genomes]
rs16909919	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066829	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236406	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236407	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274692	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297086	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297088	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28457763	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28495472	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28496034	0.82[ASN][1000 genomes]
rs28504650	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28536201	0.84[ASN][1000 genomes]
rs28557305	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620532	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28620668	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28629854	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28701981	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3758302	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4448343	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1053434	chr9:98248328-98259178	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98226000-98251000	Weak transcription	Osteobl	bone
3	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
6	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:98239400-98251400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:98239600-98253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:98240400-98256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:98241200-98248800	Weak transcription	Colonic Mucosa	Colon
15	chr9:98242000-98251200	Weak transcription	K562	blood
16	chr9:98242000-98256400	Weak transcription	Esophagus	oesophagus
17	chr9:98242200-98256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:98242400-98253400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:98242400-98253600	Weak transcription	Spleen	Spleen
20	chr9:98242400-98256200	Weak transcription	NHLF	lung
21	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
22	chr9:98242600-98256200	Weak transcription	Placenta	Placenta
23	chr9:98242800-98253800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:98242800-98256600	Weak transcription	Fetal Kidney	kidney
25	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
26	chr9:98243000-98248800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:98243000-98253800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr9:98243000-98253800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr9:98243000-98255800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:98243000-98256200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:98243000-98256800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
33	chr9:98243200-98249000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr9:98243400-98253600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:98243400-98256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:98243600-98253400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:98243600-98256400	Weak transcription	HepG2	liver
38	chr9:98243800-98249800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:98243800-98260000	Weak transcription	HSMM	muscle
40	chr9:98244000-98255600	Weak transcription	GM12878-XiMat	blood
41	chr9:98244400-98251000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:98244400-98256600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:98244800-98251400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:98244800-98257000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:98245000-98256800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:98245200-98256600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:98246000-98250000	Genic enhancers	Fetal Lung	lung
48	chr9:98246400-98249200	Enhancers	Psoas Muscle	Psoas
49	chr9:98246400-98249800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr9:98246400-98250200	Genic enhancers	Fetal Stomach	stomach

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