Variant report

Variant	rs235270
Chromosome Location	chr21:46213081-46213082
allele	G/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46208115..46211415-chr21:46211594..46214545,4	MCF-7	breast:
2	chr21:45930036..45931060-chr21:46212690..46213923,8	MCF-7	breast:
3	chr21:46212986..46216283-chr21:46290808..46295304,6	MCF-7	breast:
4	chr21:46202815..46206353-chr21:46211210..46215151,6	K562	blood:
5	chr21:45557514..45558447-chr21:46212556..46213412,2	K562	blood:
6	chr21:46212466..46215146-chr21:46219897..46223000,3	MCF-7	breast:
7	chr21:46212672..46215534-chr21:46357420..46360250,2	K562	blood:
8	chr21:45929815..45931043-chr21:46212927..46213850,6	K562	blood:
9	chr21:46207093..46209545-chr21:46210264..46213746,3	K562	blood:
10	chr21:46197899..46200792-chr21:46212721..46215023,2	MCF-7	breast:
11	chr21:45929533..45931060-chr21:46212791..46213895,9	MCF-7	breast:
12	chr21:46211611..46213164-chr21:46493063..46494889,2	K562	blood:
13	chr21:46211786..46214681-chr21:46493090..46494686,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236519	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000235890	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1060564	0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569	0.94[CHB][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13049333	0.94[CHB][hapmap];0.83[YRI][hapmap]
rs180317	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs183518	0.88[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184633	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329902	0.94[CHB][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs235267	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235268	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs235269	0.96[ASN][1000 genomes]
rs235271	0.94[CHB][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235272	0.94[CHB][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235275	0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235337	0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235352	0.88[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs235353	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs235358	0.94[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235360	0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235361	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235369	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838695	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3788134	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs434608	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs657730	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs658657	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs690626	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7280306	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs84188	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs235270	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
3	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr21:46198800-46219600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr21:46198800-46220000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:46198800-46220000	Weak transcription	Fetal Kidney	kidney
8	chr21:46200000-46220400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:46200400-46218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:46201200-46220400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:46202400-46219200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr21:46203400-46220000	Weak transcription	Fetal Brain Female	brain
13	chr21:46205200-46213200	Weak transcription	Esophagus	oesophagus
14	chr21:46205200-46220400	Weak transcription	Aorta	Aorta
15	chr21:46205200-46220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:46206200-46216200	Weak transcription	Placenta	Placenta
17	chr21:46206200-46218400	Weak transcription	Brain Anterior Caudate	brain
18	chr21:46206200-46219800	Weak transcription	Right Ventricle	heart
19	chr21:46206200-46220000	Weak transcription	Brain Germinal Matrix	brain
20	chr21:46206400-46220000	Weak transcription	Brain Hippocampus Middle	brain
21	chr21:46206800-46220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:46209800-46217800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr21:46210000-46220000	Weak transcription	Fetal Brain Male	brain
24	chr21:46210200-46220000	Weak transcription	NH-A	brain
25	chr21:46210400-46213200	Strong transcription	Dnd41	blood
26	chr21:46211000-46214200	Enhancers	Liver	Liver
27	chr21:46211200-46214000	Strong transcription	A549	lung
28	chr21:46211400-46213200	Strong transcription	Primary B cells from cord blood	blood
29	chr21:46211400-46214400	Enhancers	HepG2	liver
30	chr21:46211600-46213200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr21:46211600-46220400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr21:46211800-46220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr21:46212000-46213600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:46212000-46214200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr21:46212000-46214200	Enhancers	Fetal Intestine Small	intestine
36	chr21:46212000-46220000	Weak transcription	Lung	lung
37	chr21:46212000-46220400	Weak transcription	Colonic Mucosa	Colon
38	chr21:46212200-46214400	Strong transcription	Hela-S3	cervix
39	chr21:46212200-46216000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr21:46212400-46213400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr21:46212400-46213400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr21:46212400-46213400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr21:46212400-46213400	Enhancers	Adipose Nuclei	Adipose
44	chr21:46212400-46214200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr21:46212400-46214400	Enhancers	Fetal Intestine Large	intestine
46	chr21:46212400-46216000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr21:46212400-46217600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr21:46212400-46220400	Weak transcription	Spleen	Spleen
49	chr21:46212600-46213200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr21:46212600-46213200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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