Variant report

Variant	rs822038
Chromosome Location	chr7:129065477-129065478
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	chr7:129063475..129066777-chr7:129072113..129074429,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128578	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1000676	0.90[CHD][hapmap];0.91[JPT][hapmap]
rs10248810	0.95[JPT][hapmap]
rs10954226	0.95[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs10954230	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs10954231	0.87[ASN][1000 genomes]
rs11979476	0.91[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12112374	0.91[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs12534372	0.84[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12540568	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs12667132	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs12668958	0.85[JPT][hapmap]
rs1526900	0.95[JPT][hapmap]
rs1559486	0.95[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1880854	0.82[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs2303303	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303304	0.93[ASN][1000 genomes]
rs2694572	0.95[JPT][hapmap]
rs2694574	0.94[JPT][hapmap]
rs2718083	0.90[JPT][hapmap]
rs2718084	0.91[CEU][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs28636722	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4728163	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs4728164	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs4731572	0.90[CHD][hapmap];0.91[JPT][hapmap]
rs4731575	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs57263220	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs598412	0.85[ASW][hapmap];0.80[CHB][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs644723	0.80[CHB][hapmap]
rs6467233	0.95[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap]
rs6467243	0.86[EUR][1000 genomes]
rs66479871	0.90[ASN][1000 genomes]
rs66538149	0.80[EUR][1000 genomes]
rs66864889	0.80[EUR][1000 genomes]
rs67520056	0.83[EUR][1000 genomes]
rs68076553	0.80[EUR][1000 genomes]
rs68187585	0.86[EUR][1000 genomes]
rs691124	0.80[CHB][hapmap];0.84[TSI][hapmap]
rs691158	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs691435	0.80[CHB][hapmap];0.84[TSI][hapmap]
rs691807	0.80[AMR][1000 genomes]
rs692697	0.85[ASW][hapmap];0.80[CHB][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs6946288	0.86[ASN][1000 genomes]
rs6946938	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6948252	0.82[EUR][1000 genomes]
rs6953598	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6966595	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6971917	0.80[EUR][1000 genomes]
rs6980385	0.91[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs7788327	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs7789697	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7792317	0.82[EUR][1000 genomes]
rs7803052	0.80[EUR][1000 genomes]
rs7806089	0.82[EUR][1000 genomes]
rs822039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891545	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs963465	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs9641846	0.82[CEU][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv3391047	chr7:129064062-129066576	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs822038	UBE2H	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129008400-129073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr7:129016000-129071400	Weak transcription	Small Intestine	intestine
3	chr7:129017400-129069200	Weak transcription	Stomach Mucosa	stomach
4	chr7:129017400-129073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:129018400-129070000	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:129019400-129070800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:129019800-129066200	Weak transcription	Thymus	Thymus
8	chr7:129027800-129070200	Weak transcription	HepG2	liver
9	chr7:129028400-129073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:129029000-129070000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:129029200-129073200	Weak transcription	Brain Angular Gyrus	brain
12	chr7:129029600-129067400	Weak transcription	Fetal Brain Male	brain
13	chr7:129033800-129073600	Weak transcription	Right Ventricle	heart
14	chr7:129034200-129066200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:129035600-129072600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:129035600-129073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:129041400-129066200	Weak transcription	Esophagus	oesophagus
18	chr7:129041400-129067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:129041600-129073400	Weak transcription	HMEC	breast
20	chr7:129041800-129066000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:129042000-129066000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:129042600-129066200	Weak transcription	Gastric	stomach
23	chr7:129043400-129066400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:129043400-129072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:129046600-129066200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:129046600-129066200	Weak transcription	Aorta	Aorta
27	chr7:129046600-129073400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:129048600-129073000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr7:129049600-129073400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:129052600-129068800	Weak transcription	Fetal Kidney	kidney
31	chr7:129052600-129073200	Weak transcription	GM12878-XiMat	blood
32	chr7:129054000-129069000	Weak transcription	Fetal Lung	lung
33	chr7:129054200-129066000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:129055000-129066200	Weak transcription	Fetal Muscle Leg	muscle
35	chr7:129057200-129066800	Weak transcription	Fetal Intestine Small	intestine
36	chr7:129058200-129072400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:129058600-129070400	Weak transcription	HSMM	muscle
38	chr7:129059400-129069400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr7:129060200-129072600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr7:129061000-129072000	Weak transcription	A549	lung
41	chr7:129061200-129072600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr7:129061400-129067400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr7:129061400-129068600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr7:129061400-129069400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr7:129061600-129072000	Weak transcription	NHDF-Ad	bronchial
46	chr7:129061800-129068600	Strong transcription	Liver	Liver
47	chr7:129061800-129070000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:129062000-129067000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:129062000-129068600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:129062000-129069800	Strong transcription	Primary T cells from cord blood	blood

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