Variant report

Variant	rs28620668
Chromosome Location	chr9:98267746-98267747
allele	G/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	TEAD4	chr9:98267340-98267783	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr9:98267312-98274672	IMR90	lung:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
3	CTCF	chr9:98267336-98268145	K562	blood:	n/a	n/a
4	POLR2A	chr9:98267712-98267832	MCF10A-Er-Src	breast:	n/a	n/a
5	SIN3A	chr9:98266518-98275316	H1-hESC	embryonic stem cell:	n/a	chr9:98268478-98268491 chr9:98273259-98273270 chr9:98273104-98273113 chr9:98271212-98271225 chr9:98270756-98270767 chr9:98271270-98271279 chr9:98272257-98272268 chr9:98273102-98273111 chr9:98271251-98271264
6	CHD1	chr9:98267470-98268834	H1-hESC	embryonic stem cell:	n/a	n/a
7	SREBP1	chr9:98267175-98269407	GM12878	blood:	n/a	n/a
8	NFIC	chr9:98267739-98268874	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr9:98267718-98267918	MCF10A-Er-Src	breast:	n/a	n/a
10	REST	chr9:98267183-98274539	H1-neurons	neurons:	n/a	chr9:98270976-98270989 chr9:98268273-98268286 chr9:98271222-98271240 chr9:98270100-98270109 chr9:98270699-98270717 chr9:98271458-98271466 chr9:98268565-98268575 chr9:98271242-98271255 chr9:98269758-98269778
11	MTA3	chr9:98267734-98268194	GM12878	blood:	n/a	n/a
12	IRF1	chr9:98267645-98268891	K562	blood:	n/a	chr9:98267733-98267743 chr9:98267729-98267743 chr9:98267731-98267745 chr9:98267733-98267744
13	MAZ	chr9:98267684-98272191	IMR90	lung:	n/a	chr9:98269402-98269412 chr9:98268933-98268942
14	POLR2A	chr9:98267742-98270561	SK-N-MC	brain:	n/a	n/a
15	MAZ	chr9:98267631-98270596	GM12878	blood:	n/a	chr9:98269402-98269412 chr9:98268933-98268942
16	MXI1	chr9:98267369-98275571	SK-N-SH	brain:	n/a	chr9:98273104-98273113 chr9:98269404-98269413
17	JUND	chr9:98267713-98269326	GM12878	blood:	n/a	chr9:98268055-98268069
18	MYC	chr9:98267473-98270521	K562	blood:	n/a	chr9:98269402-98269412 chr9:98268933-98268942
19	JUND	chr9:98267471-98268601	H1-hESC	embryonic stem cell:	n/a	chr9:98268055-98268069
20	CHD1	chr9:98266325-98275163	IMR90	lung:	n/a	chr9:98271086-98271096 chr9:98274530-98274540

No.	Distal block	Cell Line	Cell type
1	chr9:98188569..98190136-chr9:98266994..98268557,2	MCF-7	breast:
2	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
3	chr9:98078830..98081414-chr9:98266391..98270806,3	MCF-7	breast:
4	chr9:98246124..98248586-chr9:98264978..98268110,3	K562	blood:
5	chr9:98187685..98192036-chr9:98266677..98274746,12	MCF-7	breast:
6	chr9:98187278..98190652-chr9:98265637..98273315,6	K562	blood:
7	chr9:98210232..98214386-chr9:98264282..98269915,4	K562	blood:
8	chr9:98253772..98257280-chr9:98266534..98270044,4	K562	blood:
9	chr9:98266714..98268433-chr9:98632145..98634773,2	MCF-7	breast:
10	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:
11	chr9:98187644..98190286-chr9:98266151..98268622,2	K562	blood:

Variant related genes	Relation type
ENSG00000271155	TF binding region
PTCH1	TF binding region
ENSG00000158169	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000237857	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10512248	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355619	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355620	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909919	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066829	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236407	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282042	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297086	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2297088	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28457763	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495472	0.83[ASN][1000 genomes]
rs28496034	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28504650	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28536201	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557305	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28591501	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28629854	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758302	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448343	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119276	0.87[AFR][1000 genomes];0.82[AMR][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	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
5	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
6	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
7	esv3327711	chr9:98266981-98273279	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3403378	chr9:98267156-98269704	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
2	chr9:98263000-98267800	Weak transcription	Placenta	Placenta
3	chr9:98263000-98267800	Weak transcription	Lung	lung
4	chr9:98264600-98268000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:98264600-98268000	Weak transcription	Gastric	stomach
6	chr9:98265600-98267800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:98265800-98268600	Weak transcription	Stomach Mucosa	stomach
8	chr9:98265800-98271600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr9:98266400-98267800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:98266400-98267800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:98266400-98267800	Enhancers	Colon Smooth Muscle	Colon
12	chr9:98266400-98268000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:98266400-98268000	Transcr. at gene 5' and 3'	Fetal Lung	lung
14	chr9:98266400-98271600	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr9:98266600-98267800	Enhancers	Adipose Nuclei	Adipose
16	chr9:98266600-98267800	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr9:98266600-98267800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:98266600-98267800	Flanking Active TSS	K562	blood
19	chr9:98266600-98268000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:98266600-98268000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:98266600-98268000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr9:98266600-98275000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr9:98266800-98267800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr9:98266800-98267800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:98266800-98267800	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr9:98266800-98268600	Active TSS	Colonic Mucosa	Colon
27	chr9:98266800-98270000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:98267000-98267800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:98267000-98267800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:98267000-98267800	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr9:98267000-98267800	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr9:98267000-98267800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr9:98267000-98267800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr9:98267000-98267800	Weak transcription	Right Ventricle	heart
35	chr9:98267000-98267800	Flanking Active TSS	Hela-S3	cervix
36	chr9:98267000-98268000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:98267000-98268000	Flanking Active TSS	Fetal Brain Female	brain
38	chr9:98267000-98268600	Active TSS	Fetal Stomach	stomach
39	chr9:98267000-98269800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr9:98267000-98270400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr9:98267000-98274800	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr9:98267200-98267800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr9:98267200-98267800	Weak transcription	Pancreas	Pancrea
44	chr9:98267200-98267800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:98267200-98267800	Flanking Active TSS	A549	lung
46	chr9:98267200-98268000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:98267200-98268000	Weak transcription	Esophagus	oesophagus
48	chr9:98267200-98273600	Active TSS	Right Atrium	heart
49	chr9:98267200-98274000	Active TSS	Fetal Intestine Large	intestine
50	chr9:98267200-98274200	Active TSS	Left Ventricle	heart

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