Variant report

Variant	rs28615746
Chromosome Location	chr9:6411160-6411161
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	RUNX3	chr9:6410936-6411293	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6410972..6413613-chr9:6564070..6565701,2	MCF-7	breast:
2	chr9:6408551..6411662-chr9:6412630..6415165,4	MCF-7	breast:

Variant related genes	Relation type
UHRF2	TF binding region
ENSG00000178445	Chromatin interaction
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10115294	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10123605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10125313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1037885	0.96[EUR][1000 genomes]
rs1048279	0.92[EUR][1000 genomes]
rs10491838	0.96[EUR][1000 genomes]
rs10739096	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739101	0.96[EUR][1000 genomes]
rs10739103	0.96[EUR][1000 genomes]
rs10739104	0.96[EUR][1000 genomes]
rs10758762	0.96[EUR][1000 genomes]
rs10758763	0.96[EUR][1000 genomes]
rs10758768	1.00[EUR][1000 genomes]
rs10758782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10815400	1.00[EUR][1000 genomes]
rs10815401	1.00[EUR][1000 genomes]
rs10815429	0.91[EUR][1000 genomes]
rs10815430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10815431	0.92[AFR][1000 genomes]
rs1156869	0.96[EUR][1000 genomes]
rs12346381	0.84[EUR][1000 genomes]
rs1322170	0.85[EUR][1000 genomes]
rs13283687	0.92[EUR][1000 genomes]
rs13284392	0.83[EUR][1000 genomes]
rs13285152	0.92[EUR][1000 genomes]
rs13285458	0.92[EUR][1000 genomes]
rs13291494	0.92[EUR][1000 genomes]
rs13293015	0.87[EUR][1000 genomes]
rs13293673	0.87[EUR][1000 genomes]
rs13296481	0.92[EUR][1000 genomes]
rs13298872	1.00[EUR][1000 genomes]
rs13299896	0.92[EUR][1000 genomes]
rs13302032	0.92[EUR][1000 genomes]
rs1330381	1.00[EUR][1000 genomes]
rs1381038	0.96[EUR][1000 genomes]
rs1407357	0.96[EUR][1000 genomes]
rs1407358	0.96[EUR][1000 genomes]
rs1412420	0.92[EUR][1000 genomes]
rs1854709	0.92[EUR][1000 genomes]
rs1855022	0.88[EUR][1000 genomes]
rs2000198	0.92[EUR][1000 genomes]
rs2019737	0.96[EUR][1000 genomes]
rs2051003	0.92[EUR][1000 genomes]
rs2150964	0.85[EUR][1000 genomes]
rs2150971	0.92[EUR][1000 genomes]
rs2381438	0.87[EUR][1000 genomes]
rs2890707	0.96[EUR][1000 genomes]
rs34530211	0.92[EUR][1000 genomes]
rs34581400	0.92[EUR][1000 genomes]
rs35301257	0.92[EUR][1000 genomes]
rs35408061	0.92[EUR][1000 genomes]
rs36089474	0.92[EUR][1000 genomes]
rs3847262	0.96[EUR][1000 genomes]
rs3858051	0.96[EUR][1000 genomes]
rs4008347	1.00[EUR][1000 genomes]
rs424119	0.96[EUR][1000 genomes]
rs4475552	0.87[EUR][1000 genomes]
rs4742172	1.00[EUR][1000 genomes]
rs4742177	0.96[EUR][1000 genomes]
rs4742180	1.00[EUR][1000 genomes]
rs4742198	0.96[EUR][1000 genomes]
rs4742200	0.96[EUR][1000 genomes]
rs4742203	0.96[EUR][1000 genomes]
rs503315	0.96[EUR][1000 genomes]
rs553048	0.92[EUR][1000 genomes]
rs6477060	0.92[EUR][1000 genomes]
rs6477067	0.96[EUR][1000 genomes]
rs67541153	0.96[EUR][1000 genomes]
rs7021445	1.00[EUR][1000 genomes]
rs7031407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031967	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032411	0.82[EUR][1000 genomes]
rs7035574	0.92[EUR][1000 genomes]
rs7036990	0.96[EUR][1000 genomes]
rs7039968	0.96[EUR][1000 genomes]
rs7040374	0.92[EUR][1000 genomes]
rs7043824	0.96[EUR][1000 genomes]
rs7043887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7044749	0.96[EUR][1000 genomes]
rs7048431	0.87[EUR][1000 genomes]
rs72693587	0.92[EUR][1000 genomes]
rs7350177	1.00[EUR][1000 genomes]
rs7851921	1.00[EUR][1000 genomes]
rs7852138	1.00[EUR][1000 genomes]
rs7853322	0.96[EUR][1000 genomes]
rs7858373	0.96[EUR][1000 genomes]
rs7859139	0.96[EUR][1000 genomes]
rs7864212	0.96[EUR][1000 genomes]
rs7869419	0.92[EUR][1000 genomes]
rs7873206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs898673	0.96[EUR][1000 genomes]
rs922221	1.00[EUR][1000 genomes]
rs980849	1.00[EUR][1000 genomes]
rs980850	0.92[EUR][1000 genomes]
rs993952	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1023419	chr9:6393886-6415025	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6405400-6412200	Weak transcription	Thymus	Thymus
2	chr9:6407000-6411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:6408200-6412200	Weak transcription	Primary T cells from cord blood	blood
4	chr9:6408800-6411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:6408800-6412200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:6408800-6412400	Weak transcription	Pancreas	Pancrea
7	chr9:6409000-6412200	Weak transcription	NHEK	skin
8	chr9:6409800-6412400	Weak transcription	Liver	Liver
9	chr9:6410000-6412200	Enhancers	Primary B cells from peripheral blood	blood
10	chr9:6410000-6412400	Enhancers	Primary B cells from cord blood	blood
11	chr9:6410000-6412600	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:6410600-6412000	Weak transcription	Fetal Stomach	stomach
13	chr9:6410600-6412200	Weak transcription	Brain Angular Gyrus	brain
14	chr9:6410600-6412400	Enhancers	GM12878-XiMat	blood
15	chr9:6410800-6411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:6410800-6412200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:6410800-6412200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:6411000-6412200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:6411000-6412200	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links