Variant report

Variant	rs1475980
Chromosome Location	chr22:33996202-33996203
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	chr22:33994236..33996382-chr22:34011754..34014539,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12628513	0.81[ASN][1000 genomes]
rs1475984	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16992562	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16992592	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs2267235	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs2267237	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs2413195	0.82[CHD][hapmap]
rs5994776	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs5999027	0.88[YRI][hapmap]
rs7290435	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7293114	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs738972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs743730	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8135942	0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv914983	chr22:33800119-34035034	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1060283	chr22:33809137-34043739	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv544684	chr22:33809137-34043739	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
13	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv914987	chr22:33920421-34047427	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv588934	chr22:33965639-34035034	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv914988	chr22:33975998-34083987	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv934161	chr22:33979015-34118621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1475980	LARGE	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33965200-34045800	Weak transcription	Pancreas	Pancrea
2	chr22:33981800-34006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr22:33981800-34006800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr22:33985200-34001800	Weak transcription	Gastric	stomach
5	chr22:33985400-33997400	Weak transcription	Brain Angular Gyrus	brain
6	chr22:33985400-34009400	Weak transcription	GM12878-XiMat	blood
7	chr22:33988600-34019200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr22:33988600-34020800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr22:33989400-34005800	Weak transcription	Colon Smooth Muscle	Colon
10	chr22:33989600-33996600	Weak transcription	Ovary	ovary
11	chr22:33989600-34000800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr22:33989600-34020400	Weak transcription	Fetal Intestine Large	intestine
13	chr22:33990000-34001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:33990000-34006200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr22:33990200-33998000	Weak transcription	HSMM	muscle
16	chr22:33990400-34001600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr22:33990400-34003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:33992200-34006800	Weak transcription	Fetal Intestine Small	intestine
19	chr22:33992800-34001800	Weak transcription	Brain Substantia Nigra	brain
20	chr22:33994000-34001800	Weak transcription	Right Atrium	heart
21	chr22:33994000-34006000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr22:33994000-34029600	Weak transcription	Aorta	Aorta
23	chr22:33994200-33997000	Weak transcription	Esophagus	oesophagus
24	chr22:33994200-33997200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr22:33994200-34000600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:33994200-34002000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr22:33994200-34010600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr22:33994200-34020600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr22:33994200-34050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr22:33994400-34002400	Weak transcription	Brain Hippocampus Middle	brain
31	chr22:33994400-34003600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr22:33994800-33997000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr22:33995000-33998800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:33995200-33996600	Strong transcription	Liver	Liver
35	chr22:33995200-34000000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:33995200-34000000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr22:33995400-33996800	Enhancers	Right Ventricle	heart
38	chr22:33995400-33997400	Enhancers	Left Ventricle	heart
39	chr22:33995400-34000600	Strong transcription	Fetal Stomach	stomach
40	chr22:33995600-33996400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr22:33995600-33996800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr22:33995600-34000600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:33995600-34008200	Weak transcription	HSMMtube	muscle
44	chr22:33995800-33997400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr22:33995800-33997600	Enhancers	Fetal Heart	heart
46	chr22:33995800-34001200	Weak transcription	Fetal Muscle Leg	muscle
47	chr22:33995800-34007000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr22:33995800-34049800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr22:33996000-33997200	Weak transcription	Fetal Lung	lung
50	chr22:33996000-33997800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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