Variant report

Variant	rs1060564
Chromosome Location	chr21:46191174-46191175
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	chr21:46188637..46191346-chr21:46209977..46212870,2	MCF-7	breast:
2	chr21:46182776..46184894-chr21:46189262..46192289,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11569	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13049333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs180317	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184633	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329902	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs235267	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235268	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235269	0.95[ASN][1000 genomes]
rs235270	0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235271	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235337	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235353	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235360	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235361	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235369	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3788134	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434608	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657730	0.90[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs658657	0.90[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs660385	0.96[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs690626	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7280306	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs84188	0.93[AMR][1000 genomes];0.96[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
rs1060564	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	chr21:46185800-46192600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr21:46185800-46199600	Weak transcription	Stomach Mucosa	stomach
3	chr21:46186200-46199400	Weak transcription	Right Atrium	heart
4	chr21:46187000-46193000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:46187000-46193200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr21:46187000-46195400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr21:46187200-46194600	Weak transcription	NHDF-Ad	bronchial
9	chr21:46187200-46197800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:46187600-46196200	Strong transcription	Thymus	Thymus
11	chr21:46187800-46196600	Strong transcription	Right Ventricle	heart
12	chr21:46187800-46199000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr21:46187800-46206200	Strong transcription	Fetal Thymus	thymus
14	chr21:46188000-46193000	Strong transcription	Fetal Intestine Small	intestine
15	chr21:46188000-46193400	Strong transcription	Lung	lung
16	chr21:46188000-46195800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr21:46188000-46196800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr21:46188000-46198800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:46188000-46199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:46188000-46201600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr21:46188000-46203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr21:46188000-46203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr21:46188200-46193400	Strong transcription	Placenta	Placenta
27	chr21:46188200-46195000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr21:46188200-46197000	Strong transcription	Fetal Brain Female	brain
29	chr21:46188200-46197200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr21:46188200-46197200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr21:46188200-46197400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr21:46188200-46198800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr21:46188200-46199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr21:46188200-46199800	Strong transcription	Primary T cells from cord blood	blood
35	chr21:46188200-46201600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr21:46188400-46191200	Strong transcription	HSMM	muscle
37	chr21:46188400-46193400	Strong transcription	Esophagus	oesophagus
38	chr21:46188400-46193400	Strong transcription	Fetal Muscle Leg	muscle
39	chr21:46188400-46194800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr21:46188400-46196000	Strong transcription	Ovary	ovary
41	chr21:46188400-46196800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr21:46188400-46197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr21:46188400-46198600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr21:46188400-46198600	Strong transcription	Adipose Nuclei	Adipose
45	chr21:46188400-46199400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr21:46188600-46197400	Strong transcription	Liver	Liver
47	chr21:46188600-46198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr21:46188600-46200200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr21:46188600-46201600	Strong transcription	Fetal Stomach	stomach
50	chr21:46188600-46208000	Strong transcription	Monocytes-CD14+_RO01746	blood

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