Variant report

Variant	rs6458769
Chromosome Location	chr6:13360638-13360639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13306050..13307672-chr6:13360364..13362318,2	K562	blood:
2	chr6:13358275..13360679-chr6:13575096..13577524,3	MCF-7	breast:
3	chr6:13357478..13359612-chr6:13359699..13362212,2	K562	blood:
4	chr6:13353670..13357830-chr6:13359815..13362315,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D7-2	chr6:13358067-13361194	NONHSAT107804

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs508477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55942054	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119181	1.00[EUR][1000 genomes]
rs57991391	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60477577	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903516	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926072	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821301	0.82[EUR][1000 genomes]
rs9463694	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr6:13350800-13364600	Weak transcription	Aorta	Aorta
2	chr6:13355400-13364000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:13355600-13383400	Weak transcription	A549	lung
4	chr6:13356000-13364400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:13356000-13364400	Weak transcription	Stomach Mucosa	stomach
6	chr6:13356200-13360800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:13356200-13360800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:13356200-13360800	Weak transcription	Fetal Brain Female	brain
9	chr6:13356200-13361000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:13356200-13361000	Weak transcription	Psoas Muscle	Psoas
11	chr6:13356200-13361000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:13356200-13362800	Weak transcription	Liver	Liver
13	chr6:13356200-13362800	Weak transcription	Fetal Kidney	kidney
14	chr6:13356200-13362800	Weak transcription	Fetal Lung	lung
15	chr6:13356200-13364000	Weak transcription	Esophagus	oesophagus
16	chr6:13356200-13364400	Weak transcription	Pancreas	Pancrea
17	chr6:13356200-13364600	Weak transcription	Lung	lung
18	chr6:13356200-13364800	Weak transcription	Colonic Mucosa	Colon
19	chr6:13356200-13365000	Weak transcription	Gastric	stomach
20	chr6:13356200-13367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:13356200-13371800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:13356200-13372000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:13356200-13373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:13356200-13378200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:13356400-13361800	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:13356400-13365000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:13356400-13368000	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:13357200-13364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:13357400-13361600	Enhancers	Primary B cells from cord blood	blood
30	chr6:13357600-13361000	Enhancers	Brain Angular Gyrus	brain
31	chr6:13357800-13361000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:13357800-13361000	Weak transcription	HUVEC	blood vessel
33	chr6:13358000-13364400	Weak transcription	Brain Germinal Matrix	brain
34	chr6:13358000-13364400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:13358000-13364600	Weak transcription	Primary T cells from cord blood	blood
36	chr6:13358000-13364600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:13358000-13364800	Weak transcription	Dnd41	blood
38	chr6:13358000-13371800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:13358200-13360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:13358200-13361000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:13358200-13362800	Weak transcription	NHLF	lung
42	chr6:13358200-13364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:13358200-13364600	Weak transcription	Thymus	Thymus
44	chr6:13358200-13367600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:13358200-13368200	Weak transcription	HMEC	breast
46	chr6:13358400-13360800	Weak transcription	Fetal Thymus	thymus
47	chr6:13358400-13360800	Weak transcription	Spleen	Spleen
48	chr6:13358400-13361200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr6:13358400-13362400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:13358400-13367600	Weak transcription	NH-A	brain

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