Variant report

Variant	rs2560814
Chromosome Location	chr6:13471445-13471446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13471062..13472931-chr6:13486374..13489089,2	MCF-7	breast:
2	chr6:13465251..13472690-chr6:13481619..13489131,10	K562	blood:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2560812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58054832	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59330070	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62385807	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62385808	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6906273	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2560814	C6orf114	cis	parietal	SCAN
rs2560814	RANBP9	cis	parietal	SCAN
rs2560814	ENSG00000187461	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13452200-13483400	Weak transcription	Gastric	stomach
2	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
3	chr6:13455200-13484400	Weak transcription	Small Intestine	intestine
4	chr6:13455200-13484600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:13455400-13481000	Weak transcription	HUVEC	blood vessel
6	chr6:13462800-13484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:13463200-13481000	Weak transcription	A549	lung
8	chr6:13463400-13476600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:13463600-13473200	Weak transcription	HepG2	liver
10	chr6:13463600-13484400	Weak transcription	Primary T cells from cord blood	blood
11	chr6:13463800-13484600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:13464600-13476400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:13465200-13485000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:13466400-13473400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:13466800-13474200	Weak transcription	Hela-S3	cervix
16	chr6:13467000-13478600	Weak transcription	Thymus	Thymus
17	chr6:13467200-13473800	Weak transcription	Primary B cells from cord blood	blood
18	chr6:13467800-13472800	Weak transcription	Fetal Thymus	thymus
19	chr6:13467800-13473400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:13467800-13474800	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:13468000-13471800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:13468000-13472000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:13468000-13473400	Weak transcription	Esophagus	oesophagus
24	chr6:13468200-13472000	Weak transcription	K562	blood
25	chr6:13468200-13474000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:13468200-13474600	Weak transcription	Liver	Liver
27	chr6:13468200-13477000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:13469000-13471800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:13469200-13473600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:13469200-13480000	Weak transcription	Aorta	Aorta
31	chr6:13469400-13485800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:13469800-13471800	Strong transcription	NHEK	skin
33	chr6:13469800-13472200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:13470000-13471600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:13470000-13471600	Enhancers	Fetal Heart	heart
36	chr6:13470000-13471800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:13470000-13473200	Enhancers	NHDF-Ad	bronchial
38	chr6:13470000-13474200	Enhancers	Right Atrium	heart
39	chr6:13470200-13471800	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr6:13470200-13471800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:13470200-13471800	Enhancers	Fetal Brain Male	brain
42	chr6:13470200-13471800	Enhancers	Left Ventricle	heart
43	chr6:13470200-13472000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:13470200-13472000	Enhancers	Brain Germinal Matrix	brain
45	chr6:13470400-13471600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr6:13470400-13471600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:13470400-13471800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr6:13470400-13471800	Enhancers	Fetal Brain Female	brain
49	chr6:13470400-13471800	Enhancers	Fetal Muscle Trunk	muscle
50	chr6:13470400-13471800	Enhancers	Lung	lung

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