Variant report

Variant	rs10843459
Chromosome Location	chr12:9496402-9496403
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9494429..9497191-chr12:9497385..9498990,2	MCF-7	breast:
2	chr11:62379397..62380044-chr12:9496046..9496903,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PZP-10	chr12:9495983-9496596	NONHSAT026583

Variant related genes	Relation type
ENSG00000149499	Chromatin interaction
ENSG00000149489	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11049986	1.00[CHB][hapmap]
rs11050246	1.00[ASN][1000 genomes]
rs11050254	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050303	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050304	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050310	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050397	0.89[ASN][1000 genomes]
rs11050527	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11050586	0.89[ASN][1000 genomes]
rs11050592	0.89[ASN][1000 genomes]
rs11050604	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11050605	0.89[ASN][1000 genomes]
rs11836204	1.00[CHB][hapmap]
rs12366751	0.87[EUR][1000 genomes]
rs12370449	0.89[ASN][1000 genomes]
rs12372791	0.89[ASN][1000 genomes]
rs17804080	1.00[CHB][hapmap]
rs17804845	0.89[ASN][1000 genomes]
rs17804911	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2113904	0.89[ASN][1000 genomes]
rs2194829	0.89[ASN][1000 genomes]
rs34591612	0.89[ASN][1000 genomes]
rs36132622	0.89[ASN][1000 genomes]
rs4883242	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55635549	0.89[ASN][1000 genomes]
rs55693818	0.89[ASN][1000 genomes]
rs56004061	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56014159	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56236944	1.00[ASN][1000 genomes]
rs7295431	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302181	1.00[ASN][1000 genomes]
rs73047561	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310088	1.00[JPT][hapmap]
rs7315769	1.00[JPT][hapmap]
rs7486338	0.89[ASN][1000 genomes]
rs9668938	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv898742	chr12:9473157-9518222	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9490200-9504400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:9490800-9500000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9492400-9497000	Weak transcription	Fetal Brain Male	brain
4	chr12:9492800-9500200	Enhancers	Primary T cells from cord blood	blood
5	chr12:9493000-9496800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:9493200-9502400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:9493400-9500400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:9493600-9496600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:9493800-9496600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:9493800-9496800	Strong transcription	Fetal Lung	lung
11	chr12:9494000-9499400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:9494000-9499400	Weak transcription	Osteobl	bone
13	chr12:9494000-9502600	Weak transcription	HSMM	muscle
14	chr12:9495000-9497800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:9495600-9497000	Enhancers	HepG2	liver
16	chr12:9495600-9497800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:9495600-9498600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:9495800-9497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:9495800-9498400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:9496000-9497000	Enhancers	Fetal Muscle Leg	muscle
21	chr12:9496200-9496600	Enhancers	Brain Substantia Nigra	brain
22	chr12:9496200-9496600	Enhancers	Fetal Stomach	stomach
23	chr12:9496200-9496600	Enhancers	Ovary	ovary
24	chr12:9496200-9499000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:9496200-9500800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:9496400-9497000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:9496400-9498800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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