Variant report

Variant	rs4819147
Chromosome Location	chr21:47162321-47162322
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	chr21:47161212..47163794-chr21:47166078..47168615,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11089019	0.90[ASN][1000 genomes]
rs11908836	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11911348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs2015400	0.93[CEU][hapmap]
rs2330328	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2838977	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2838979	0.90[ASN][1000 genomes]
rs2839008	0.87[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs2839023	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2839024	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs4819138	0.80[CHB][hapmap]
rs4819142	0.90[CHB][hapmap]
rs4819160	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs725930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7278258	0.82[CHB][hapmap]
rs7280089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232746	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232764	0.82[EUR][1000 genomes]
rs741954	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs8133338	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs9798668	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs9977594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs9982063	0.87[ASN][1000 genomes]
rs9982174	0.87[ASN][1000 genomes]
rs9984438	0.87[CEU][hapmap];0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4819147	KRTAP10-5	cis	parietal	SCAN
rs4819147	PCBP3	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47135600-47165000	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:47151800-47164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:47153200-47165400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr21:47156600-47168000	Weak transcription	Brain Angular Gyrus	brain
6	chr21:47156800-47164800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:47157000-47168200	Weak transcription	Brain Hippocampus Middle	brain
8	chr21:47157600-47165000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:47157800-47167400	Weak transcription	HSMMtube	muscle
10	chr21:47158000-47165400	Weak transcription	Dnd41	blood
11	chr21:47158800-47169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr21:47159000-47168000	Weak transcription	Brain Anterior Caudate	brain
13	chr21:47160000-47164800	Weak transcription	Thymus	Thymus
14	chr21:47160200-47164200	Weak transcription	Fetal Thymus	thymus
15	chr21:47160600-47165600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:47160600-47165600	Weak transcription	Gastric	stomach
17	chr21:47160800-47162400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:47160800-47165800	Weak transcription	Adipose Nuclei	Adipose
19	chr21:47161200-47165000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr21:47161400-47164800	Weak transcription	Spleen	Spleen
21	chr21:47161400-47165400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr21:47161400-47165400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr21:47161400-47165600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr21:47161600-47162400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr21:47161600-47162400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:47161800-47162600	Enhancers	NHEK	skin
27	chr21:47162000-47162400	Enhancers	HMEC	breast
28	chr21:47162000-47164600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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