Variant report

Variant	rs878560
Chromosome Location	chr6:13378536-13378537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13378331..13380363-chr6:13384667..13386393,2	K562	blood:
2	chr6:13378332..13381749-chr6:13612503..13616973,4	MCF-7	breast:
3	chr6:13374615..13376910-chr6:13377833..13379393,2	K562	blood:
4	chr6:13376403..13381150-chr6:13486389..13489473,5	MCF-7	breast:
5	chr6:13374146..13377100-chr6:13377431..13379906,2	MCF-7	breast:
6	chr6:13376520..13380811-chr6:13573724..13576714,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10948641	1.00[EUR][1000 genomes]
rs11754614	1.00[EUR][1000 genomes]
rs11755431	1.00[EUR][1000 genomes]
rs11756942	1.00[EUR][1000 genomes]
rs11758235	1.00[EUR][1000 genomes]
rs11759443	1.00[EUR][1000 genomes]
rs2439559	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2496171	1.00[EUR][1000 genomes]
rs28495821	1.00[EUR][1000 genomes]
rs4452644	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs526661	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6911459	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6912427	1.00[EUR][1000 genomes]
rs6920849	1.00[EUR][1000 genomes]
rs6925659	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73359121	1.00[EUR][1000 genomes]
rs754439	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7742713	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9463696	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9474025	0.84[ASW][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9474036	1.00[EUR][1000 genomes]
rs9474040	1.00[EUR][1000 genomes]
rs9474061	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9474068	0.84[AFR][1000 genomes];1.00[AMR][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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13355600-13383400	Weak transcription	A549	lung
2	chr6:13365400-13379800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:13365800-13378800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:13365800-13378800	Weak transcription	Gastric	stomach
5	chr6:13365800-13379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:13365800-13379600	Weak transcription	Brain Germinal Matrix	brain
7	chr6:13365800-13380600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:13366000-13378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:13366000-13380600	Weak transcription	Ovary	ovary
11	chr6:13366000-13382800	Weak transcription	Liver	Liver
12	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:13368200-13381000	Weak transcription	NH-A	brain
15	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:13372200-13380600	Weak transcription	Lung	lung
17	chr6:13372400-13381000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:13372800-13379000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:13372800-13380600	Weak transcription	Fetal Brain Female	brain
20	chr6:13372800-13380800	Weak transcription	Fetal Brain Male	brain
21	chr6:13373000-13379200	Weak transcription	Brain Angular Gyrus	brain
22	chr6:13373000-13379200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:13373200-13378800	Weak transcription	Right Atrium	heart
24	chr6:13373600-13379400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:13374200-13379200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:13374200-13380800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:13374400-13379000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:13374400-13379200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:13374400-13379200	Weak transcription	Fetal Heart	heart
30	chr6:13374400-13380400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:13375600-13379200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:13376000-13379000	Weak transcription	Esophagus	oesophagus
33	chr6:13376000-13383400	Weak transcription	Psoas Muscle	Psoas
34	chr6:13376200-13379200	Weak transcription	HUVEC	blood vessel
35	chr6:13376200-13381600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:13376400-13381200	Weak transcription	HMEC	breast
37	chr6:13376600-13379400	Weak transcription	Adipose Nuclei	Adipose
38	chr6:13376800-13378600	Weak transcription	Right Ventricle	heart
39	chr6:13376800-13386600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:13376800-13395200	Weak transcription	NHEK	skin
41	chr6:13377000-13378600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:13377400-13380200	Enhancers	Primary B cells from peripheral blood	blood
43	chr6:13377600-13379800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr6:13377600-13380200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:13377800-13378600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:13377800-13379000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:13377800-13379200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr6:13377800-13379400	Enhancers	Primary B cells from cord blood	blood
49	chr6:13377800-13383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:13377800-13395600	Weak transcription	Aorta	Aorta

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