Variant report

Variant	rs2838487
Chromosome Location	chr21:45508288-45508289
allele	A/C
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	chr21:45506516-45509197	K562	blood:	n/a	n/a
2	POLR2A	chr21:45506914-45508389	HL-60	blood:	n/a	n/a
3	POLR2A	chr21:45507846-45508664	K562	blood:	n/a	n/a
4	POLR2A	chr21:45508199-45509291	GM12892	blood:	n/a	n/a
5	POLR2A	chr21:45507941-45509266	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:45507953-45508443	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
TRAPPC10	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11910604	0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2020943	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2071144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071145	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2227265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838463	1.00[TSI][hapmap]
rs2838465	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2838470	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838484	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2838497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2838510	0.85[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs28834388	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57812760	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57855582	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60503863	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61689295	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62226718	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62226719	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62226722	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62226723	0.92[EUR][1000 genomes]
rs62226724	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7275501	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7282644	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73909115	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8128926	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878132	1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9284512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306175	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9974767	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9975436	1.00[EUR][1000 genomes]
rs9977122	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9977460	0.88[ASN][1000 genomes]
rs9978109	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9978772	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9979931	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9980021	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9980063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9982695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs9982907	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9983551	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9983596	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9984876	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer 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	32 gene(s)	inside rSNPs	diseases
9	nsv459294	chr21:45499171-45595060	Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv587722	chr21:45499171-45595060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838487	PWP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45445400-45509400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45473000-45526600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr21:45481600-45510800	Strong transcription	Dnd41	blood
4	chr21:45481600-45523800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr21:45486200-45524000	Strong transcription	GM12878-XiMat	blood
6	chr21:45488400-45523800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:45491200-45510800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:45491400-45514600	Strong transcription	Osteobl	bone
9	chr21:45491600-45514600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr21:45492600-45510800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr21:45493000-45508400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr21:45493000-45510400	Strong transcription	HSMM	muscle
13	chr21:45493000-45510800	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr21:45493400-45514800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr21:45493600-45510800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr21:45493600-45510800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr21:45493600-45515000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr21:45493800-45514400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr21:45494000-45510800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr21:45495600-45526800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr21:45496200-45510800	Strong transcription	Fetal Brain Female	brain
22	chr21:45496200-45514200	Strong transcription	Brain Germinal Matrix	brain
23	chr21:45496200-45514600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr21:45497000-45510000	Weak transcription	Psoas Muscle	Psoas
25	chr21:45497400-45514600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr21:45498000-45512400	Strong transcription	HMEC	breast
27	chr21:45498400-45524000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr21:45498600-45511000	Strong transcription	HepG2	liver
29	chr21:45498600-45512400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr21:45498600-45523800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr21:45498800-45510800	Strong transcription	NH-A	brain
32	chr21:45499000-45523600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr21:45499000-45524000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr21:45502600-45509600	Genic enhancers	Right Ventricle	heart
35	chr21:45503400-45514600	Genic enhancers	Fetal Intestine Small	intestine
36	chr21:45503600-45524200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr21:45503800-45510000	Genic enhancers	Liver	Liver
38	chr21:45503800-45510400	Strong transcription	NHEK	skin
39	chr21:45504000-45508800	Genic enhancers	Lung	lung
40	chr21:45504000-45510600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr21:45504200-45524200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr21:45504600-45510800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr21:45504600-45514400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr21:45504600-45524800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr21:45504800-45510800	Genic enhancers	Fetal Thymus	thymus
46	chr21:45504800-45514400	Strong transcription	Fetal Muscle Leg	muscle
47	chr21:45505000-45510600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:45505000-45510800	Strong transcription	Esophagus	oesophagus
49	chr21:45505000-45514200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr21:45505200-45508600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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