Variant report

Variant	rs12003252
Chromosome Location	chr9:15480144-15480145
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15478298..15480267-chr9:15506894..15508631,2	K562	blood:
2	chr9:15478524..15480549-chr9:15486729..15489229,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12000752	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12001476	0.87[YRI][hapmap]
rs12001490	0.87[YRI][hapmap]
rs12001969	0.85[LWK][hapmap];1.00[AMR][1000 genomes]
rs12002581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12003556	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12003712	1.00[AMR][1000 genomes]
rs12004985	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12005949	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12006227	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12006472	1.00[AMR][1000 genomes]
rs35722073	1.00[AMR][1000 genomes]
rs35982923	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6474919	0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7858863	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:15439000-15492200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:15442800-15508400	Strong transcription	Fetal Thymus	thymus
4	chr9:15443000-15482200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:15444000-15482000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
12	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:15444800-15482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:15448200-15482200	Weak transcription	Psoas Muscle	Psoas
16	chr9:15449000-15492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
18	chr9:15452200-15480200	Weak transcription	Brain Substantia Nigra	brain
19	chr9:15452200-15492400	Weak transcription	Right Ventricle	heart
20	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:15456200-15480600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:15457000-15482000	Strong transcription	Dnd41	blood
23	chr9:15457000-15492400	Weak transcription	Lung	lung
24	chr9:15459000-15492200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
26	chr9:15461000-15492200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:15461600-15483800	Weak transcription	Fetal Intestine Small	intestine
28	chr9:15461600-15492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:15461600-15492800	Weak transcription	Pancreas	Pancrea
30	chr9:15462200-15482200	Weak transcription	Brain Angular Gyrus	brain
31	chr9:15462800-15505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:15466200-15492400	Weak transcription	Gastric	stomach
33	chr9:15466600-15492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:15467200-15501000	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:15467400-15505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:15468800-15480600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:15468800-15482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:15468800-15483800	Weak transcription	Fetal Stomach	stomach
39	chr9:15468800-15484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:15468800-15484600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:15468800-15492400	Weak transcription	Colonic Mucosa	Colon
42	chr9:15468800-15492400	Weak transcription	Spleen	Spleen
43	chr9:15469200-15491800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr9:15469200-15505600	Weak transcription	NHLF	lung
45	chr9:15469800-15486400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:15470400-15480600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr9:15470400-15485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr9:15471000-15492600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr9:15472200-15509000	Weak transcription	HMEC	breast
50	chr9:15472800-15480600	Weak transcription	Aorta	Aorta

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