Variant report

Variant	rs2555575
Chromosome Location	chr8:67375519-67375520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:67373363..67378961-chr8:67380708..67384244,6	MCF-7	breast:
2	chr8:67374151..67375671-chr8:67623910..67626033,2	MCF-7	breast:
3	chr8:67373454..67375848-chr8:67443609..67445864,2	MCF-7	breast:
4	chr8:67370426..67372835-chr8:67375511..67377950,2	K562	blood:
5	chr8:67371423..67376205-chr8:67520601..67527002,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185697	Chromatin interaction
ENSG00000147576	Chromatin interaction
ENSG00000169085	Chromatin interaction
ENSG00000104205	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1025228	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1030419	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1060242	0.87[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs10957372	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1108	0.84[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs12541098	0.84[JPT][hapmap]
rs13682	0.86[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1426907	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1426908	0.85[CHB][hapmap]
rs1963852	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2059640	0.87[EUR][1000 genomes]
rs2059641	0.87[EUR][1000 genomes]
rs2059642	0.87[EUR][1000 genomes]
rs2357894	0.81[EUR][1000 genomes]
rs2465982	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2465984	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2465985	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465986	0.84[ASN][1000 genomes]
rs2465987	0.84[ASN][1000 genomes]
rs2465990	0.87[EUR][1000 genomes]
rs2555565	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555569	0.87[EUR][1000 genomes]
rs2555570	0.87[EUR][1000 genomes]
rs2555571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555572	0.87[EUR][1000 genomes]
rs2555574	0.87[EUR][1000 genomes]
rs2555582	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555587	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718988	0.90[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718990	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs2719000	0.87[EUR][1000 genomes]
rs2719002	0.84[EUR][1000 genomes]
rs2719004	0.87[EUR][1000 genomes]
rs2719005	0.87[EUR][1000 genomes]
rs2719006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005366	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs753082	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs890515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9693689	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3446467	chr8:66749863-67667068	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3414665	chr8:66936816-67381935	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv6236	chr8:67359312-67403981	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv465702	chr8:67375519-67385088	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv611457	chr8:67375519-67385088	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2555575	ADHFE1	cis	multi-tissue	Pritchard
rs2555575	C8orf46	cis	Nerve Tibial	GTEx
rs2555575	ADHFE1	cis	Nerve Tibial	GTEx
rs2555575	C8orf46	cis	Skin Sun Exposed Lower leg	GTEx
rs2555575	ADHFE1	cis	cerebellum	SCAN
rs2555575	C8orf46	cis	Adipose Subcutaneous	GTEx
rs2555575	C8orf46	cis	Esophagus Muscularis	GTEx
rs2555575	C8orf46	cis	lung	GTEx
rs2555575	MYBL1	cis	parietal	SCAN
rs2555575	C8orf46	cis	Stomach	GTEx
rs2555575	ADHFE1	cis	Artery Tibial	GTEx
rs2555575	ADHFE1	cis	Muscle Skeletal	GTEx
rs2555575	ADHFE1	cis	parietal	SCAN
rs2555575	C8orf46	cis	Artery Tibial	GTEx
rs2555575	C8orf46	cis	Thyroid	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:67359400-67384400	Weak transcription	Fetal Kidney	kidney
2	chr8:67361400-67377400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:67364400-67375800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr8:67364600-67378800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr8:67364800-67384000	Weak transcription	Colon Smooth Muscle	Colon
6	chr8:67365200-67377400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr8:67365400-67383800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr8:67365800-67379600	Weak transcription	Esophagus	oesophagus
9	chr8:67366000-67376600	Weak transcription	Right Atrium	heart
10	chr8:67368400-67384400	Weak transcription	Psoas Muscle	Psoas
11	chr8:67369000-67375800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:67369000-67376000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr8:67369000-67376000	Weak transcription	Fetal Heart	heart
14	chr8:67370800-67384200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr8:67371200-67383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:67371400-67384200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr8:67372000-67376800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:67372200-67377600	Strong transcription	Adipose Nuclei	Adipose
19	chr8:67372400-67375600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:67372400-67375800	Weak transcription	NHEK	skin
21	chr8:67372400-67377000	Strong transcription	Ovary	ovary
22	chr8:67372400-67378800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr8:67372600-67375600	Weak transcription	HMEC	breast
24	chr8:67372600-67377800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:67372600-67381000	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr8:67372600-67383600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr8:67372800-67375800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:67372800-67378200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:67372800-67380200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr8:67372800-67381400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr8:67372800-67383600	Weak transcription	Brain Hippocampus Middle	brain
32	chr8:67372800-67384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:67372800-67395200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr8:67373000-67384400	Weak transcription	Brain Angular Gyrus	brain
35	chr8:67373200-67376800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr8:67373400-67377200	Strong transcription	Brain Substantia Nigra	brain
37	chr8:67373600-67376000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr8:67373600-67380400	Weak transcription	Fetal Muscle Leg	muscle
39	chr8:67373800-67375600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr8:67373800-67376000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:67373800-67379800	Weak transcription	Gastric	stomach
42	chr8:67373800-67385400	Weak transcription	Fetal Intestine Small	intestine
43	chr8:67374000-67375600	Weak transcription	Fetal Stomach	stomach
44	chr8:67374000-67376800	Genic enhancers	Placenta	Placenta
45	chr8:67374000-67379200	Weak transcription	Brain Anterior Caudate	brain
46	chr8:67374000-67381200	Weak transcription	Spleen	Spleen
47	chr8:67374400-67376800	Genic enhancers	Liver	Liver
48	chr8:67374400-67382200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr8:67374800-67375600	Enhancers	A549	lung
50	chr8:67374800-67375800	Enhancers	Stomach Smooth Muscle	stomach

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