Variant report

Variant	rs2821530
Chromosome Location	chr9:15478776-15478777
allele	A/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	POLR2A	chr9:15478357-15478862	K562	blood:	n/a	n/a

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:

Variant related genes	Relation type
PSIP1	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10116904	0.83[EUR][1000 genomes]
rs10117375	0.85[AMR][1000 genomes]
rs10117803	0.92[AMR][1000 genomes]
rs10117823	0.94[YRI][hapmap];0.92[AMR][1000 genomes]
rs10118595	0.83[EUR][1000 genomes]
rs10118675	0.83[EUR][1000 genomes]
rs10118719	0.81[EUR][1000 genomes]
rs10119931	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10120171	0.83[EUR][1000 genomes]
rs10121012	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10121911	0.83[EUR][1000 genomes]
rs10123084	0.83[EUR][1000 genomes]
rs10123651	0.93[YRI][hapmap];0.92[AMR][1000 genomes]
rs10124718	0.83[EUR][1000 genomes]
rs10125713	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1041529	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10962054	0.93[AMR][1000 genomes]
rs12336383	0.84[AMR][1000 genomes]
rs12336445	0.84[AMR][1000 genomes]
rs12337310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344963	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12348561	0.85[EUR][1000 genomes]
rs12348564	0.85[EUR][1000 genomes]
rs12348780	0.85[EUR][1000 genomes]
rs12350062	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12350903	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12352398	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12353048	0.85[EUR][1000 genomes]
rs12859	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs175762	0.93[AMR][1000 genomes]
rs1882939	0.97[EUR][1000 genomes]
rs2064030	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2221706	0.84[AMR][1000 genomes]
rs2490852	0.85[AMR][1000 genomes]
rs2665503	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2665510	0.97[EUR][1000 genomes]
rs2665511	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2665512	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2665515	0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2737840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276437	0.84[AMR][1000 genomes]
rs276438	0.85[AMR][1000 genomes]
rs276445	0.92[AMR][1000 genomes]
rs276446	0.92[AMR][1000 genomes]
rs276450	0.92[AMR][1000 genomes]
rs276451	0.92[AMR][1000 genomes]
rs2777949	1.00[ASN][1000 genomes]
rs2777951	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2795123	0.97[EUR][1000 genomes]
rs2795124	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2795125	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2795127	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795128	1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs2798701	0.85[AMR][1000 genomes]
rs2798717	0.92[AMR][1000 genomes]
rs2821525	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2821529	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2821533	0.97[EUR][1000 genomes]
rs2821542	0.85[AMR][1000 genomes]
rs2821543	0.92[AMR][1000 genomes]
rs2821544	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28497163	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28610358	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28659858	0.84[AMR][1000 genomes]
rs28796681	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28800775	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28805077	0.85[AMR][1000 genomes]
rs28808908	0.83[EUR][1000 genomes]
rs28844368	0.83[EUR][1000 genomes]
rs28882210	0.83[EUR][1000 genomes]
rs3119700	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3122701	0.84[AMR][1000 genomes]
rs3122705	0.92[AMR][1000 genomes]
rs3129711	0.92[AMR][1000 genomes]
rs365710	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs381205	0.85[AMR][1000 genomes]
rs392627	0.84[AMR][1000 genomes]
rs413356	0.92[AMR][1000 genomes]
rs415157	0.85[AMR][1000 genomes]
rs418153	0.92[AMR][1000 genomes]
rs4237140	0.84[AMR][1000 genomes]
rs443563	0.82[EUR][1000 genomes]
rs592452	0.85[AMR][1000 genomes]
rs7021840	0.91[EUR][1000 genomes]
rs741930	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852936	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7860339	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs796391	0.92[AMR][1000 genomes]
rs811282	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs909323	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs926154	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9298729	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:124 , 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	chr9:15443200-15479600	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:15443200-15490400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:15443200-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:15443400-15479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:15443800-15492200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:15444000-15482000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:15444000-15487600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:15444000-15492400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:15444400-15495200	Weak transcription	Fetal Heart	heart
14	chr9:15444600-15491200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:15444800-15482200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:15447000-15509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:15448200-15482200	Weak transcription	Psoas Muscle	Psoas
18	chr9:15448400-15480000	Weak transcription	Stomach Mucosa	stomach
19	chr9:15449000-15492200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:15449800-15509000	Weak transcription	Small Intestine	intestine
21	chr9:15452200-15480200	Weak transcription	Brain Substantia Nigra	brain
22	chr9:15452200-15492400	Weak transcription	Right Ventricle	heart
23	chr9:15454600-15508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:15456200-15480600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:15457000-15482000	Strong transcription	Dnd41	blood
26	chr9:15457000-15492400	Weak transcription	Lung	lung
27	chr9:15459000-15492200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr9:15460800-15510000	Weak transcription	Esophagus	oesophagus
29	chr9:15461000-15492200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:15461600-15483800	Weak transcription	Fetal Intestine Small	intestine
31	chr9:15461600-15492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:15461600-15492800	Weak transcription	Pancreas	Pancrea
33	chr9:15462200-15482200	Weak transcription	Brain Angular Gyrus	brain
34	chr9:15462800-15505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:15466200-15492400	Weak transcription	Gastric	stomach
36	chr9:15466600-15492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:15467200-15501000	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:15467400-15505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:15468800-15480600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:15468800-15482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr9:15468800-15483800	Weak transcription	Fetal Stomach	stomach
42	chr9:15468800-15484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:15468800-15484600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:15468800-15492400	Weak transcription	Colonic Mucosa	Colon
45	chr9:15468800-15492400	Weak transcription	Spleen	Spleen
46	chr9:15469200-15480000	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:15469200-15491800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:15469200-15505600	Weak transcription	NHLF	lung
49	chr9:15469800-15486400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:15470000-15479400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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