Variant report

Variant	rs3788136
Chromosome Location	chr21:46186698-46186699
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46183165..46184854-chr21:46185530..46187850,2	K562	blood:
2	chr21:46021562..46023632-chr21:46186668..46188181,2	K562	blood:
3	chr21:46185007..46187777-chr21:46197158..46201208,5	MCF-7	breast:
4	chr21:46184586..46187452-chr21:46187793..46189728,3	MCF-7	breast:
5	chr21:46185632..46187378-chr21:46187744..46189857,2	K562	blood:
6	chr21:46181841..46189587-chr21:46189919..46197097,16	MCF-7	breast:
7	chr21:46171917..46177806-chr21:46181342..46188371,13	MCF-7	breast:
8	chr21:46185600..46187229-chr21:46198465..46200138,2	MCF-7	breast:
9	chr21:46184622..46186979-chr21:46203808..46205316,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1071792	0.92[EUR][1000 genomes]
rs11088963	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1109280	0.95[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11701732	0.85[ASN][1000 genomes]
rs13049657	0.86[JPT][hapmap]
rs13050872	0.81[JPT][hapmap]
rs1347324	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1821431	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294157	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2329899	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2329900	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2838673	0.85[EUR][1000 genomes]
rs2838675	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs2838678	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838686	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35209090	0.91[ASN][1000 genomes]
rs35242981	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35933313	0.91[ASN][1000 genomes]
rs4239838	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818734	0.86[JPT][hapmap]
rs4818973	0.86[EUR][1000 genomes]
rs4818974	0.86[EUR][1000 genomes]
rs4818975	1.00[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62220109	0.88[ASN][1000 genomes]
rs62222752	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6518204	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7281735	0.84[ASN][1000 genomes]
rs733161	0.86[EUR][1000 genomes]
rs760431	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs760432	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8103	1.00[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8128992	0.82[EUR][1000 genomes]
rs8133039	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs885655	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs885656	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs885657	0.80[CEU][hapmap];0.86[EUR][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
rs3788136	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46181200-46188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr21:46181800-46188000	Weak transcription	Fetal Intestine Small	intestine
3	chr21:46181800-46188400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr21:46182200-46189000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr21:46182400-46187000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr21:46182600-46188600	Weak transcription	Liver	Liver
7	chr21:46183600-46190800	Weak transcription	A549	lung
8	chr21:46183800-46186800	Enhancers	Esophagus	oesophagus
9	chr21:46184400-46187200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr21:46184400-46187400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr21:46184600-46186800	Enhancers	Placenta	Placenta
12	chr21:46184600-46186800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:46184600-46187200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr21:46184600-46187600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr21:46184600-46189000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr21:46184600-46189200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr21:46184800-46186800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr21:46184800-46187000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr21:46184800-46187000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr21:46184800-46187000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr21:46184800-46188000	Weak transcription	Lung	lung
22	chr21:46184800-46188600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:46184800-46188800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr21:46184800-46188800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:46184800-46189600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr21:46185000-46186800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr21:46185000-46187000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr21:46185000-46187000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:46185000-46188000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr21:46185000-46188200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr21:46185200-46188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr21:46185200-46188000	Weak transcription	Brain Germinal Matrix	brain
33	chr21:46185200-46189000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr21:46185200-46189600	Weak transcription	NHLF	lung
35	chr21:46185400-46187000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr21:46185600-46187400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr21:46185600-46187400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr21:46185600-46188000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr21:46185600-46188200	Weak transcription	Primary T cells from cord blood	blood
40	chr21:46185600-46188200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr21:46185600-46190800	Weak transcription	Brain Anterior Caudate	brain
42	chr21:46185600-46190800	Weak transcription	Hela-S3	cervix
43	chr21:46185800-46186800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr21:46185800-46186800	Enhancers	HepG2	liver
45	chr21:46185800-46187400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr21:46185800-46187600	Weak transcription	Thymus	Thymus
47	chr21:46185800-46188000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr21:46185800-46188000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr21:46185800-46188000	Weak transcription	Fetal Brain Female	brain
50	chr21:46185800-46188400	Weak transcription	Adipose Nuclei	Adipose

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