Variant report

Variant	rs28520278
Chromosome Location	chr4:166162885-166162886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10005213	0.98[ASN][1000 genomes]
rs10009579	1.00[ASN][1000 genomes]
rs10010264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10015050	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10019675	1.00[CEU][hapmap]
rs10022944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10213218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213277	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12108446	0.83[ASN][1000 genomes]
rs12108624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331117	1.00[ASN][1000 genomes]
rs28397216	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28495546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28525405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28621585	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28641126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs28669375	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28685193	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28853353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6834112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7665057	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9761388	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991944	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9992742	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9996084	0.93[ASN][1000 genomes]
rs9999376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv966337	chr4:166157947-166176361	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
2	chr4:166130400-166176800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:166130600-166200800	Weak transcription	Lung	lung
4	chr4:166131600-166165800	Weak transcription	Gastric	stomach
5	chr4:166131600-166196800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:166132200-166193800	Weak transcription	Fetal Brain Female	brain
7	chr4:166136000-166176800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:166137800-166194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:166138200-166168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:166138400-166185600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:166142800-166165800	Weak transcription	Esophagus	oesophagus
12	chr4:166142800-166176800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:166144000-166163200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:166144000-166165000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:166144000-166165400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:166144000-166176000	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:166144200-166168800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:166144200-166168800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:166144200-166168800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:166144600-166218800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:166144800-166176200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:166147000-166165400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:166147000-166176400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:166151200-166168400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:166151200-166176000	Weak transcription	Dnd41	blood
26	chr4:166151400-166168400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:166152000-166163200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:166152000-166176600	Weak transcription	Fetal Stomach	stomach
29	chr4:166152200-166169400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:166154000-166169200	Weak transcription	HUVEC	blood vessel
31	chr4:166154600-166168800	Weak transcription	Primary T cells from cord blood	blood
32	chr4:166156200-166165600	Weak transcription	HepG2	liver
33	chr4:166156200-166199200	Weak transcription	Ovary	ovary
34	chr4:166159200-166163000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:166159200-166169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:166159400-166173200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:166159400-166175800	Weak transcription	GM12878-XiMat	blood
38	chr4:166159600-166166000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:166159800-166167200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:166159800-166170400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:166159800-166176000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:166160000-166169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:166160600-166165600	Weak transcription	Fetal Lung	lung
44	chr4:166161000-166165800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:166161000-166165800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:166161200-166165400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:166161200-166167200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:166161200-166168800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr4:166161200-166169000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:166161200-166176800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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