Variant report

Variant	rs10023867
Chromosome Location	chr4:53496551-53496552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10000311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10001370	0.94[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10003396	0.81[ASN][1000 genomes]
rs10010306	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10012676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	0.93[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10021143	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10027906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10028085	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10028755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10029145	1.00[ASN][1000 genomes]
rs10031386	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10033218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10471216	0.93[ASN][1000 genomes]
rs13434726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13435157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28376189	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28376284	1.00[AFR][1000 genomes]
rs28379922	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28380682	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28396506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402205	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28411005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28412170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28430452	0.93[ASN][1000 genomes]
rs28436702	0.87[AFR][1000 genomes]
rs28451750	1.00[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28478374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28482298	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28503210	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28514875	1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28565016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28588481	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28590396	0.93[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28644292	1.00[ASN][1000 genomes]
rs28651623	1.00[AFR][1000 genomes]
rs28654693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28660550	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28660571	0.93[ASN][1000 genomes]
rs28672279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28694544	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28711292	1.00[AFR][1000 genomes]
rs28721897	0.93[ASN][1000 genomes]
rs28722174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28784684	0.93[ASN][1000 genomes]
rs28825181	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28825412	0.93[ASN][1000 genomes]
rs28849759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28852068	0.93[ASN][1000 genomes]
rs6830833	0.93[ASN][1000 genomes]
rs7673679	0.90[ASN][1000 genomes]
rs9990686	0.93[ASN][1000 genomes]
rs9994643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9997863	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53451800-53501400	Weak transcription	Small Intestine	intestine
2	chr4:53456000-53506400	Weak transcription	HUVEC	blood vessel
3	chr4:53463000-53507200	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:53464200-53523600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:53468200-53510200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:53468600-53497600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:53472600-53499000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:53473000-53506800	Weak transcription	Primary T cells from cord blood	blood
9	chr4:53473600-53507200	Weak transcription	Osteobl	bone
10	chr4:53475000-53501200	Weak transcription	Gastric	stomach
11	chr4:53476000-53502200	Weak transcription	Pancreas	Pancrea
12	chr4:53476000-53507400	Weak transcription	HSMM	muscle
13	chr4:53476600-53501600	Weak transcription	HepG2	liver
14	chr4:53477600-53510200	Weak transcription	Esophagus	oesophagus
15	chr4:53479800-53499800	Weak transcription	Right Atrium	heart
16	chr4:53480800-53499800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:53480800-53501200	Weak transcription	GM12878-XiMat	blood
18	chr4:53484600-53508400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:53485200-53498000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:53485400-53497600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:53485400-53499400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:53485800-53501600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:53485800-53507600	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:53485800-53508400	Weak transcription	Stomach Mucosa	stomach
25	chr4:53486000-53507200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:53486000-53507200	Weak transcription	Brain Substantia Nigra	brain
27	chr4:53486000-53507200	Weak transcription	Fetal Intestine Small	intestine
28	chr4:53486200-53507200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:53486400-53499200	Weak transcription	Fetal Lung	lung
30	chr4:53486600-53508800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:53487400-53504800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:53488000-53496800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:53488600-53496600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:53488800-53496800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:53489200-53503000	Weak transcription	Aorta	Aorta
36	chr4:53489200-53507000	Weak transcription	NHEK	skin
37	chr4:53489400-53507200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:53490600-53497400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:53491400-53501200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:53491800-53507000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:53492000-53503400	Weak transcription	Right Ventricle	heart
42	chr4:53492000-53507200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:53492200-53501200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:53492200-53506400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:53492200-53507200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:53492200-53507800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:53492200-53510000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr4:53492400-53498600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:53492400-53501200	Weak transcription	Ovary	ovary
50	chr4:53492400-53507000	Weak transcription	HSMMtube	muscle

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