Variant report

Variant	rs2838479
Chromosome Location	chr21:45482950-45482951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45437723..45440453-chr21:45482663..45485495,2	K562	blood:
2	chr21:45473377..45479336-chr21:45481371..45487468,11	K562	blood:

Extended variants
information (count: 54 )
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];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.81[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];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2071145	0.83[ASN][1000 genomes]
rs2227265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[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];0.92[EUR][1000 genomes];0.91[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];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838487	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]
rs2838495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes]
rs2838497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
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];0.81[MKK][hapmap]
rs28834388	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57812760	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57855582	0.83[ASN][1000 genomes]
rs60503863	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61689295	0.84[EUR][1000 genomes]
rs62226718	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62226719	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62226722	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62226723	0.84[EUR][1000 genomes]
rs62226724	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7275501	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7282644	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73909115	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8128926	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs878132	1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9284512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9306175	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9974767	0.89[ASN][1000 genomes]
rs9975436	0.92[EUR][1000 genomes]
rs9977122	0.92[EUR][1000 genomes];0.98[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];0.85[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9978772	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9979931	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9980021	0.84[EUR][1000 genomes];0.83[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];0.92[EUR][1000 genomes]
rs9982907	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9983551	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9983596	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984876	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1064549	chr21:45446358-45493720	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838479	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	chr21:45446400-45502200	Weak transcription	Fetal Heart	heart
3	chr21:45451000-45494400	Weak transcription	Fetal Brain Male	brain
4	chr21:45458200-45483000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr21:45459400-45483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:45463400-45485200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr21:45463600-45485000	Strong transcription	Thymus	Thymus
8	chr21:45465200-45485200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr21:45465800-45485000	Strong transcription	Fetal Thymus	thymus
10	chr21:45465800-45487800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr21:45466000-45484400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr21:45468400-45502400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr21:45468800-45502600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:45469400-45487000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr21:45469400-45502000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr21:45471400-45487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:45471800-45495400	Strong transcription	Fetal Muscle Leg	muscle
18	chr21:45471800-45502200	Strong transcription	Fetal Intestine Small	intestine
19	chr21:45472000-45494200	Weak transcription	Psoas Muscle	Psoas
20	chr21:45472000-45502600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr21:45472400-45491200	Strong transcription	Fetal Intestine Large	intestine
22	chr21:45472600-45483200	Weak transcription	Stomach Mucosa	stomach
23	chr21:45472600-45504400	Strong transcription	Fetal Stomach	stomach
24	chr21:45472800-45503800	Strong transcription	Liver	Liver
25	chr21:45473000-45485200	Weak transcription	Colon Smooth Muscle	Colon
26	chr21:45473000-45526600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr21:45474800-45485200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr21:45475000-45493000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr21:45475000-45502600	Weak transcription	Right Atrium	heart
30	chr21:45475200-45487600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:45475200-45494000	Weak transcription	Fetal Kidney	kidney
32	chr21:45475600-45485800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr21:45475600-45491200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr21:45476200-45487600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr21:45476400-45485000	Weak transcription	NHDF-Ad	bronchial
36	chr21:45478200-45483000	Weak transcription	Brain Substantia Nigra	brain
37	chr21:45478200-45483200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr21:45478200-45487000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr21:45478600-45483000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr21:45478600-45483000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr21:45478600-45483800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr21:45478800-45483400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr21:45478800-45484400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr21:45479000-45483600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr21:45479400-45483600	Weak transcription	Aorta	Aorta
46	chr21:45479800-45491200	Weak transcription	Small Intestine	intestine
47	chr21:45480000-45483000	Weak transcription	Pancreas	Pancrea
48	chr21:45480000-45483000	Weak transcription	HUVEC	blood vessel
49	chr21:45480000-45483200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr21:45480000-45484400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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