Variant report

Variant	rs12003885
Chromosome Location	chr9:95709210-95709211
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	POLR2A	chr9:95709162-95709352	H1-hESC	embryonic stem cell:	n/a	n/a
2	NFATC1	chr9:95709044-95709449	GM12878	blood:	n/a	n/a
3	SUZ12	chr9:95708997-95709401	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:95709160-95709372	Gliobla	brain:	n/a	n/a
5	KAP1	chr9:95708756-95709867	HEK293	kidney:	n/a	n/a
6	PBX3	chr9:95709159-95709460	GM12878	blood:	n/a	n/a
7	BCL3	chr9:95709099-95709483	GM12878	blood:	n/a	n/a
8	ZBTB7A	chr9:95709203-95710581	ECC-1	luminal epithelium:	n/a	n/a
9	REST	chr9:95709052-95711028	H1-neurons	neurons:	n/a	chr9:95709946-95709959 chr9:95709583-95709596 chr9:95709704-95709717

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95708784..95711358-chr9:96213029..96214881,2	K562	blood:

Variant related genes	Relation type
FGD3	TF binding region
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12003440	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13284600	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13293147	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13294147	0.94[ASN][1000 genomes]
rs16908645	0.81[EUR][1000 genomes]
rs17886128	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34405247	0.90[ASN][1000 genomes]
rs34739544	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34953814	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35449185	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35721889	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35861549	0.81[EUR][1000 genomes]
rs4074836	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078292	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4260949	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744160	0.90[ASN][1000 genomes]
rs58264693	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7024752	0.94[ASN][1000 genomes]
rs7035881	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7043469	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7856228	0.81[EUR][1000 genomes]
rs7856678	0.81[EUR][1000 genomes]
rs7856681	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7858810	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7859461	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873125	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9942865	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];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	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv3373273	chr9:95707031-95711229	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95702000-95709400	Weak transcription	Right Atrium	heart
2	chr9:95706400-95709400	Weak transcription	Psoas Muscle	Psoas
3	chr9:95707600-95709600	Weak transcription	Ovary	ovary
4	chr9:95709000-95709400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
5	chr9:95709000-95709400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:95709000-95709400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
7	chr9:95709000-95709400	Bivalent Enhancer	Primary B cells from cord blood	blood
8	chr9:95709000-95709400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:95709000-95709400	Enhancers	Gastric	stomach
10	chr9:95709000-95709400	Enhancers	HMEC	breast
11	chr9:95709000-95709600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr9:95709000-95709600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr9:95709000-95709600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr9:95709000-95709600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr9:95709000-95709600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr9:95709000-95709600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr9:95709000-95709600	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr9:95709000-95709800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr9:95709000-95712000	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr9:95709000-95712200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr9:95709200-95709400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr9:95709200-95709400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr9:95709200-95709400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:95709200-95709400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:95709200-95709400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:95709200-95709400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:95709200-95709400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:95709200-95709400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:95709200-95709400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr9:95709200-95709400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr9:95709200-95709400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:95709200-95709400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:95709200-95709400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
34	chr9:95709200-95709400	Enhancers	Primary hematopoietic stem cells	blood
35	chr9:95709200-95709400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:95709200-95709400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr9:95709200-95709400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:95709200-95709400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:95709200-95709400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:95709200-95709400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:95709200-95709400	Bivalent/Poised TSS	Adipose Nuclei	Adipose
42	chr9:95709200-95709400	Bivalent Enhancer	Brain Anterior Caudate	brain
43	chr9:95709200-95709400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
44	chr9:95709200-95709400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
45	chr9:95709200-95709400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
46	chr9:95709200-95709400	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr9:95709200-95709400	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
48	chr9:95709200-95709400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr9:95709200-95709400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr9:95709200-95709400	Bivalent Enhancer	Fetal Muscle Leg	muscle

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