Variant report

Variant	rs2070548
Chromosome Location	chr21:45350031-45350032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45347889..45351135-chr21:45352926..45356421,4	MCF-7	breast:
2	chr21:45223486..45226473-chr21:45348909..45351794,2	K562	blood:
3	chr21:45346418..45348065-chr21:45349559..45351638,3	K562	blood:
4	chr21:45349099..45350809-chr21:45357162..45358991,2	MCF-7	breast:
5	chr21:45283505..45286463-chr21:45348240..45352791,7	MCF-7	breast:
6	chr21:45283531..45287054-chr21:45347082..45351012,6	MCF-7	breast:
7	chr21:45341019..45344772-chr21:45346724..45351005,5	MCF-7	breast:
8	chr21:45349952..45352425-chr21:45363835..45365722,2	K562	blood:
9	chr21:45284552..45285785-chr21:45349151..45350031,4	MCF-7	breast:
10	chr21:45349394..45350688-chr21:45394837..45395974,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11700575	0.89[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs2070546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070549	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838433	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2838434	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3788075	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs3788082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819338	0.84[CHD][hapmap];0.81[MEX][hapmap]
rs4819341	0.84[ASN][1000 genomes]
rs58565118	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59355960	0.85[ASN][1000 genomes]
rs60316193	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73226931	0.86[ASN][1000 genomes]
rs9647250	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9975713	0.98[ASN][1000 genomes]
rs9983066	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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
4	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2070548	CBS	cis	cerebellum	SCAN
rs2070548	C21orf88	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45336400-45351600	Weak transcription	Fetal Brain Female	brain
2	chr21:45337200-45350800	Weak transcription	Fetal Brain Male	brain
3	chr21:45337600-45358600	Weak transcription	Osteobl	bone
4	chr21:45338800-45358600	Weak transcription	Hela-S3	cervix
5	chr21:45340800-45358800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr21:45341400-45358600	Weak transcription	A549	lung
7	chr21:45342200-45357000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr21:45342200-45358800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr21:45342400-45356400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr21:45342600-45350400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:45342600-45353000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr21:45342600-45354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr21:45342800-45350600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr21:45342800-45351000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:45343000-45357600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr21:45343000-45372400	Weak transcription	Small Intestine	intestine
17	chr21:45343400-45355200	Weak transcription	Brain Germinal Matrix	brain
18	chr21:45343400-45355600	Weak transcription	Brain Angular Gyrus	brain
19	chr21:45343600-45358000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr21:45343800-45356000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:45343800-45356200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr21:45343800-45357600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr21:45343800-45358600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:45343800-45358600	Weak transcription	HSMM	muscle
25	chr21:45343800-45358800	Weak transcription	Ovary	ovary
26	chr21:45343800-45379800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr21:45344000-45357200	Strong transcription	Fetal Stomach	stomach
28	chr21:45344200-45352200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr21:45344400-45350200	Strong transcription	Thymus	Thymus
30	chr21:45344400-45350400	Strong transcription	Dnd41	blood
31	chr21:45344400-45358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr21:45344600-45352400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr21:45345200-45358600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr21:45345400-45353000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr21:45345400-45358600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr21:45345600-45353800	Weak transcription	Colonic Mucosa	Colon
37	chr21:45345800-45351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:45345800-45352800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr21:45345800-45354800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr21:45346400-45352000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr21:45346400-45355400	Weak transcription	Fetal Lung	lung
42	chr21:45347200-45350400	Strong transcription	Primary T cells from cord blood	blood
43	chr21:45347200-45351200	Enhancers	Left Ventricle	heart
44	chr21:45347400-45350200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr21:45347400-45350200	Genic enhancers	Esophagus	oesophagus
46	chr21:45347400-45350400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr21:45347400-45350400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr21:45347400-45350800	Enhancers	Psoas Muscle	Psoas
49	chr21:45347600-45350200	Strong transcription	HepG2	liver
50	chr21:45347600-45350200	Strong transcription	NHLF	lung

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