Variant report

Variant	rs11778529
Chromosome Location	chr8:61474452-61474453
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61428999..61430549-chr8:61472398..61474659,2	MCF-7	breast:
2	chr8:61471508..61475092-chr8:61475799..61479657,3	K562	blood:

Variant related genes	Relation type
ENSG00000104388	Chromatin interaction
ENSG00000251396	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10091703	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10100740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101576	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10101714	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10103438	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10109278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110436	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435602	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10504311	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10957135	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10957136	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957137	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10957138	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957140	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957143	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10957146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774500	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11775407	0.80[EUR][1000 genomes]
rs11778708	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782463	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11784284	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11786146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11988528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12680436	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681841	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266707	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13267765	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13267828	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13269925	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13278228	0.84[YRI][hapmap]
rs1480342	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2170677	0.88[YRI][hapmap]
rs2326556	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2326557	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2625445	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28495747	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542403	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28678079	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2875966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234629	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523017	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775344	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35837434	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35853087	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592014	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610455	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621279	0.89[CEU][hapmap]
rs624407	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6471884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs649634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66983460	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669960	0.89[CEU][hapmap]
rs671275	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs677467	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6993237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6995397	0.95[CEU][hapmap]
rs6996344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998294	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7357376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462738	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812421	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7820349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7821738	0.83[YRI][hapmap]
rs7822391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7832664	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7832964	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7842105	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643524	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv3384611	chr8:61461615-61480346	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11778529	RAB2	cis	lesional skin	skin_eQTL
rs11778529	RAB2	cis	normal skin	skin_eQTL
rs11778529	RAB2A	cis	Heart Left Ventricle	GTEx
rs11778529	RAB2	cis	uninvolved skin	skin_eQTL
rs11778529	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61434800-61480600	Weak transcription	HMEC	breast
2	chr8:61438000-61488600	Weak transcription	Fetal Brain Female	brain
3	chr8:61439400-61494600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:61440800-61480000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr8:61448600-61505400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr8:61451400-61482200	Weak transcription	Right Ventricle	heart
7	chr8:61451800-61475800	Weak transcription	Fetal Heart	heart
8	chr8:61455800-61475400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr8:61457800-61475800	Weak transcription	K562	blood
10	chr8:61458200-61480600	Weak transcription	Gastric	stomach
11	chr8:61458200-61497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:61459400-61495800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr8:61463600-61482200	Weak transcription	Esophagus	oesophagus
14	chr8:61466400-61516800	Weak transcription	Stomach Mucosa	stomach
15	chr8:61466600-61474800	Weak transcription	Brain Angular Gyrus	brain
16	chr8:61467000-61476000	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:61467200-61515400	Weak transcription	Fetal Brain Male	brain
18	chr8:61468000-61482200	Weak transcription	Aorta	Aorta
19	chr8:61468800-61488600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr8:61469000-61495000	Weak transcription	Brain Germinal Matrix	brain
21	chr8:61469400-61488600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:61470000-61477200	Strong transcription	Primary T cells from cord blood	blood
23	chr8:61470200-61478000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:61470400-61476800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr8:61470600-61474600	Weak transcription	Small Intestine	intestine
26	chr8:61470800-61476400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:61470800-61477000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr8:61470800-61478000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr8:61471200-61475000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:61471200-61475000	Strong transcription	Fetal Thymus	thymus
31	chr8:61471400-61474800	Strong transcription	HSMM	muscle
32	chr8:61471400-61475200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr8:61471400-61476200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr8:61471400-61477800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr8:61471400-61477800	Strong transcription	Dnd41	blood
36	chr8:61471600-61475000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr8:61471600-61475400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr8:61471600-61477800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:61471800-61474800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr8:61471800-61474800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr8:61471800-61475200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:61471800-61476600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr8:61471800-61477800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:61472000-61474600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr8:61472000-61474800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:61472000-61476400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr8:61472000-61478000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr8:61472000-61488800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:61472400-61475200	Strong transcription	A549	lung
50	chr8:61472400-61475600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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