Variant report

Variant	rs541841
Chromosome Location	chr6:81231798-81231799
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10447324	0.84[ASN][1000 genomes]
rs10447325	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10447326	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10806194	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10943720	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11964999	0.82[ASN][1000 genomes]
rs12195284	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12195347	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12207977	0.89[ASN][1000 genomes]
rs13203786	0.89[ASN][1000 genomes]
rs2168103	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2247639	0.82[EUR][1000 genomes]
rs2322842	0.97[EUR][1000 genomes]
rs2322843	0.97[EUR][1000 genomes]
rs2603458	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2653484	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28360539	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28789711	0.83[EUR][1000 genomes]
rs2917600	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4315973	0.85[EUR][1000 genomes]
rs4394171	0.97[EUR][1000 genomes]
rs4410688	0.97[EUR][1000 genomes]
rs4527663	0.84[EUR][1000 genomes]
rs4706121	0.81[ASN][1000 genomes]
rs471335	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480295	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541037	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs549621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs577203	0.82[EUR][1000 genomes]
rs62406533	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667882	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683706	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6921723	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs6933382	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6936716	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722715	0.87[EUR][1000 genomes]
rs9449074	0.88[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs953498	0.97[EUR][1000 genomes]
rs953499	0.97[EUR][1000 genomes]
rs953500	0.96[EUR][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	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1019670	chr6:81086504-81569984	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv915714	chr6:81134888-81366749	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv886311	chr6:81166178-81239971	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv886312	chr6:81166178-81309481	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv886313	chr6:81177227-81239971	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81227000-81232800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:81227200-81232600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:81227600-81231800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:81227600-81231800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:81227600-81231800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:81227600-81232800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:81227800-81232000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:81228000-81231800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:81229800-81233200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:81230000-81231800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:81230200-81234000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:81230400-81231800	Weak transcription	NH-A	brain
13	chr6:81230400-81232400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:81230400-81232400	Weak transcription	Osteobl	bone
15	chr6:81230400-81237800	Weak transcription	Pancreas	Pancrea
16	chr6:81230600-81231800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:81230600-81231800	Weak transcription	HSMM	muscle
18	chr6:81230600-81232000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:81230600-81232600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:81230800-81232400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:81230800-81234000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:81231000-81231800	Weak transcription	NHDF-Ad	bronchial
23	chr6:81231000-81232400	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:81231000-81232800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:81231200-81232600	Enhancers	Stomach Smooth Muscle	stomach
26	chr6:81231400-81232400	Weak transcription	Brain Germinal Matrix	brain
27	chr6:81231400-81233600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:81231600-81231800	Enhancers	Rectal Smooth Muscle	rectum
29	chr6:81231600-81232400	Enhancers	Fetal Brain Female	brain
30	chr6:81231600-81233000	Enhancers	HUVEC	blood vessel
31	chr6:81231600-81233400	Enhancers	Pancreatic Islets	Pancreatic Islet

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