Variant report

Variant	rs28633576
Chromosome Location	chr9:98257305-98257306
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	CEBPB	chr9:98256957-98257329	K562	blood:	n/a	chr9:98257137-98257150 chr9:98257137-98257148 chr9:98257139-98257150
2	RUNX3	chr9:98256554-98257307	GM12878	blood:	n/a	n/a
3	MAX	chr9:98256171-98257691	NB4	blood:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
4	POLR2A	chr9:98256062-98257543	GM12892	blood:	n/a	n/a
5	MYC	chr9:98256207-98257677	NB4	blood:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
6	POLR2A	chr9:98256177-98257662	GM12892	blood:	n/a	n/a
7	CHD2	chr9:98257241-98257400	GM12878	blood:	n/a	n/a
8	CREB1	chr9:98256435-98257321	GM12878	blood:	n/a	n/a
9	RUNX3	chr9:98256525-98257352	GM12878	blood:	n/a	n/a
10	MAZ	chr9:98256610-98257597	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:98256462-98257574	GM12878	blood:	n/a	n/a
12	MAX	chr9:98256218-98257508	GM12878	blood:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
13	MTA3	chr9:98256333-98257469	GM12878	blood:	n/a	n/a
14	NRF1	chr9:98255996-98257314	SK-N-SH	brain:	n/a	chr9:98256402-98256416 chr9:98256436-98256445 chr9:98256434-98256448 chr9:98256434-98256445 chr9:98256434-98256443 chr9:98256405-98256416 chr9:98256458-98256467 chr9:98256431-98256445 chr9:98256405-98256419 chr9:98256405-98256414
15	KAP1	chr9:98257297-98257506	HEK293	kidney:	n/a	n/a
16	CEBPB	chr9:98257009-98257320	IMR90	lung:	n/a	chr9:98257137-98257150 chr9:98257137-98257148 chr9:98257139-98257150
17	MXI1	chr9:98255701-98258478	SK-N-SH	brain:	n/a	chr9:98256240-98256255 chr9:98256344-98256353
18	SMC3	chr9:98256661-98257408	GM12878	blood:	n/a	n/a
19	CEBPB	chr9:98257084-98257514	H1-hESC	embryonic stem cell:	n/a	chr9:98257137-98257150 chr9:98257137-98257148 chr9:98257139-98257150
20	ZNF384	chr9:98257023-98257308	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:98256373-98257429	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:98256393-98257362	H1-neurons	neurons:	n/a	n/a
23	NRF1	chr9:98256256-98257364	GM12878	blood:	n/a	chr9:98256402-98256416 chr9:98256436-98256445 chr9:98256434-98256448 chr9:98256434-98256445 chr9:98256434-98256443 chr9:98256405-98256416 chr9:98256458-98256467 chr9:98256431-98256445 chr9:98256405-98256419 chr9:98256405-98256414

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf102-12	chr9:98257206-98257661	ENSG00000271314.1

Variant related genes	Relation type
PTCH1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs17368876	0.85[EUR][1000 genomes]
rs17369383	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066836	0.98[ASN][1000 genomes]
rs2134721	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274693	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274694	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297087	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28394554	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28411363	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28442014	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28468571	0.81[EUR][1000 genomes]
rs28485705	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28488553	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28504341	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28571635	0.95[ASN][1000 genomes]
rs28702657	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28704635	0.80[AMR][1000 genomes]
rs62558340	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9632897	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9632898	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9632916	0.85[EUR][1000 genomes];0.88[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:105 , 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	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
8	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
9	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
10	chr9:98243800-98260000	Weak transcription	HSMM	muscle
11	chr9:98246600-98259600	Weak transcription	Right Atrium	heart
12	chr9:98248000-98258400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:98249400-98257800	Weak transcription	Liver	Liver
15	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
16	chr9:98253400-98261000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:98253400-98262400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr9:98253600-98257400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:98253600-98257600	Strong transcription	Fetal Intestine Small	intestine
20	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
21	chr9:98255600-98257400	Strong transcription	Fetal Intestine Large	intestine
22	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
23	chr9:98255800-98260200	Enhancers	Fetal Brain Male	brain
24	chr9:98256000-98257400	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr9:98256200-98257400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:98256200-98257400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:98256200-98257400	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr9:98256200-98257600	Genic enhancers	Pancreas	Pancrea
29	chr9:98256200-98257800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr9:98256200-98257800	Flanking Active TSS	GM12878-XiMat	blood
31	chr9:98256400-98257400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr9:98256400-98257400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:98256400-98257400	Enhancers	Esophagus	oesophagus
34	chr9:98256400-98257400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr9:98256400-98257400	Enhancers	Right Ventricle	heart
36	chr9:98256400-98257400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr9:98256400-98257600	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr9:98256400-98257600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr9:98256400-98257600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:98256400-98257600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:98256600-98257400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:98256600-98257400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr9:98256600-98257400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr9:98256600-98257400	Active TSS	Rectal Smooth Muscle	rectum
45	chr9:98256600-98257600	Enhancers	Fetal Heart	heart
46	chr9:98256600-98257600	Enhancers	Fetal Kidney	kidney
47	chr9:98256600-98257600	Enhancers	K562	blood
48	chr9:98256600-98257800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr9:98256600-98258400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:98256600-98259000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links