Variant report

Variant	rs180317
Chromosome Location	chr21:46196631-46196632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46191363..46195338-chr21:46195868..46201575,8	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1060564	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11569	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183518	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs184633	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2329902	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs235267	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235268	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs235269	0.93[ASN][1000 genomes]
rs235270	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235271	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235272	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235275	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235337	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235352	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235353	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235360	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235361	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235369	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838695	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3788134	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs434608	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657730	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs658657	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs660385	0.83[ASN][1000 genomes]
rs690626	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7280306	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs84188	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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
rs180317	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46185800-46199600	Weak transcription	Stomach Mucosa	stomach
2	chr21:46186200-46199400	Weak transcription	Right Atrium	heart
3	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr21:46187200-46197800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr21:46187800-46199000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:46187800-46206200	Strong transcription	Fetal Thymus	thymus
7	chr21:46188000-46196800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr21:46188000-46198800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:46188000-46199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr21:46188000-46201600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr21:46188000-46203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr21:46188000-46203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr21:46188200-46197000	Strong transcription	Fetal Brain Female	brain
17	chr21:46188200-46197200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr21:46188200-46197200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr21:46188200-46197400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:46188200-46198800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:46188200-46199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:46188200-46199800	Strong transcription	Primary T cells from cord blood	blood
23	chr21:46188200-46201600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr21:46188400-46196800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr21:46188400-46197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr21:46188400-46198600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:46188400-46198600	Strong transcription	Adipose Nuclei	Adipose
28	chr21:46188400-46199400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:46188600-46197400	Strong transcription	Liver	Liver
30	chr21:46188600-46198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr21:46188600-46200200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr21:46188600-46201600	Strong transcription	Fetal Stomach	stomach
33	chr21:46188600-46208000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr21:46189000-46198400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr21:46189000-46199600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr21:46189000-46201400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr21:46189200-46203000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr21:46189400-46198800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr21:46189400-46198800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:46189600-46197200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr21:46189600-46197800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr21:46189600-46198000	Strong transcription	NHEK	skin
44	chr21:46189600-46198200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr21:46189600-46198200	Strong transcription	HepG2	liver
46	chr21:46189600-46198600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr21:46189600-46198600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr21:46189600-46198600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr21:46189600-46198800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr21:46189600-46199000	Strong transcription	Left Ventricle	heart

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