Variant report

Variant	rs56087572
Chromosome Location	chr6:80284988-80284989
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	chr6:80284614..80287050-chr6:80339232..80342066,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGRL2-5	chr6:80283594-80285247	NONHSAT113706

Variant related genes	Relation type
ENSG00000198478	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10498921	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158770	1.00[ASN][1000 genomes]
rs1158771	1.00[ASN][1000 genomes]
rs11965020	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966497	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1485370	0.84[ASN][1000 genomes]
rs1485372	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504368	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16890774	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890835	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890850	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890862	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17335231	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727505	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575204	1.00[ASN][1000 genomes]
rs2575208	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655666	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655677	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655679	0.86[ASN][1000 genomes]
rs2655680	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655703	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2803188	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803189	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803197	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269343	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55989614	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56745436	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61152095	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411332	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411348	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413360	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413362	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62413366	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413368	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413370	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413371	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62413372	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413377	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413380	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413382	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413399	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413401	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413416	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413421	0.92[AMR][1000 genomes]
rs6454124	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454125	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907133	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917186	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921102	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934060	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73747413	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73750727	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763266	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763268	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768651	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768724	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769778	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7772722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775232	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992872	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv463906	chr6:80240951-80313297	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv604052	chr6:80240951-80313297	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80278000-80287400	Weak transcription	Small Intestine	intestine
2	chr6:80279400-80287600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80280800-80285200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:80281000-80309600	Weak transcription	Brain Angular Gyrus	brain
5	chr6:80281200-80287400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:80281200-80289600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:80283000-80285000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:80283400-80285000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:80283400-80285000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:80283400-80285000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:80283600-80285000	Enhancers	HepG2	liver
12	chr6:80283600-80285000	Enhancers	NH-A	brain
13	chr6:80283800-80285000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:80283800-80285000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:80283800-80285000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:80283800-80285000	Enhancers	HSMM	muscle
17	chr6:80283800-80285000	Enhancers	HUVEC	blood vessel
18	chr6:80284000-80285000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:80284000-80285200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:80284600-80286800	Weak transcription	Stomach Mucosa	stomach
21	chr6:80284800-80285000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:80284800-80285200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:80284800-80287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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