Variant report

Variant	rs34068461
Chromosome Location	chr6:80228535-80228536
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:79786363..79788392-chr6:80226877..80228992,2	K562	blood:
2	chr6:80225254..80226799-chr6:80227104..80230022,2	K562	blood:
3	chr6:80227058..80229732-chr6:80232396..80234486,2	MCF-7	breast:
4	chr6:80220196..80223373-chr6:80227964..80230707,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGRL2-9	chr6:80228485-80228894	NONHSAT113695

Variant related genes	Relation type
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11753205	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11756302	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11756486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11757993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758791	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1472729	0.84[EUR][1000 genomes]
rs16879583	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16890821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890842	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16890846	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1857722	0.84[EUR][1000 genomes]
rs2047897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2069304	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455943	0.84[EUR][1000 genomes]
rs2455944	0.84[EUR][1000 genomes]
rs2629469	0.81[ASN][1000 genomes]
rs2655665	0.84[EUR][1000 genomes]
rs2655686	0.84[EUR][1000 genomes]
rs2655689	0.84[EUR][1000 genomes]
rs2803172	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2803176	0.84[EUR][1000 genomes]
rs2803177	0.84[EUR][1000 genomes]
rs2803178	0.84[EUR][1000 genomes]
rs2812697	0.84[EUR][1000 genomes]
rs2812699	0.84[EUR][1000 genomes]
rs35548514	0.83[ASN][1000 genomes]
rs4706790	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4706792	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55697211	0.84[AMR][1000 genomes]
rs55951062	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56311322	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72899927	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72899942	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72899955	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72899963	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72901812	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72901839	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7743617	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7755562	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7771276	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7774418	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7775536	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9443675	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9448731	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9448733	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9448738	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv1798451	chr6:80222511-80234343	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80179800-80235000	Weak transcription	HSMMtube	muscle
2	chr6:80190200-80234400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:80195400-80235000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:80198400-80235000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:80199000-80235000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:80207600-80246000	Weak transcription	Ovary	ovary
7	chr6:80209000-80235000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:80212400-80232600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:80214400-80235000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:80214600-80246000	Weak transcription	Fetal Stomach	stomach
11	chr6:80215200-80229600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:80216000-80236800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:80216400-80235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:80216400-80235000	Weak transcription	NH-A	brain
15	chr6:80217600-80235000	Weak transcription	Pancreas	Pancrea
16	chr6:80217800-80246000	Weak transcription	Aorta	Aorta
17	chr6:80218200-80244000	Weak transcription	Fetal Brain Female	brain
18	chr6:80218400-80233800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:80219000-80235400	Weak transcription	Fetal Heart	heart
20	chr6:80220400-80230200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:80221400-80235600	Weak transcription	Fetal Kidney	kidney
22	chr6:80221800-80234400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:80222400-80235200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:80223000-80233200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:80223400-80234800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:80223400-80240400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:80223600-80233600	Weak transcription	Fetal Lung	lung
28	chr6:80223600-80234000	Weak transcription	HMEC	breast
29	chr6:80224000-80233400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:80224800-80233600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:80225800-80235000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:80227400-80234800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:80227600-80229000	Strong transcription	HSMM	muscle
34	chr6:80227800-80229800	Weak transcription	Brain Anterior Caudate	brain
35	chr6:80228000-80229000	Active TSS	K562	blood
36	chr6:80228000-80241800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:80228400-80229800	Weak transcription	Fetal Intestine Small	intestine

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