Variant report

Variant	rs12338746
Chromosome Location	chr9:3351570-3351571
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	STAT3	chr9:3351289-3351625	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RFX3	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10117357	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10117431	0.83[ASN][1000 genomes]
rs10124292	0.83[ASN][1000 genomes]
rs10124295	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10511447	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971534	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971535	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971599	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12002215	0.83[ASN][1000 genomes]
rs12347068	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13286511	0.83[ASN][1000 genomes]
rs13302664	0.83[ASN][1000 genomes]
rs16917371	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986682	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35945655	0.81[ASN][1000 genomes]
rs56829164	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66463406	0.83[ASN][1000 genomes]
rs7021584	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7022682	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026530	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029544	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043493	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7045360	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768485	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858850	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860163	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869854	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870914	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298952	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv466091	chr9:3349487-3389660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv613146	chr9:3349487-3389660	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
4	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr9:3330400-3354200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:3333000-3352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:3337800-3352600	Weak transcription	Primary B cells from cord blood	blood
8	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:3345400-3352600	Weak transcription	Fetal Lung	lung
11	chr9:3346000-3352600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:3350600-3360800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
14	chr9:3351400-3361400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links