Variant report

Variant	rs671275
Chromosome Location	chr8:61525780-61525781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61524875..61526902-chr8:61529551..61531219,2	K562	blood:
2	chr8:61525465..61527090-chr8:61529519..61532324,2	K562	blood:
3	chr8:61525760..61527520-chr8:61863383..61865720,2	K562	blood:
4	chr8:61525459..61529300-chr8:61532493..61534738,4	K562	blood:
5	chr8:61427063..61431145-chr8:61524680..61528238,3	MCF-7	breast:
6	chr8:61525175..61527465-chr8:61536083..61538610,2	K562	blood:

Variant related genes	Relation type
ENSG00000104388	Chromatin interaction
ENSG00000251396	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10091703	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10100740	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10101576	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10103438	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10109278	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10110436	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1014860	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10435602	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10957138	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10957140	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10957141	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10957143	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10957146	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10957149	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11774500	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11778529	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11778708	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11778772	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11778888	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11782178	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11782463	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11784284	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11786146	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11988528	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12678694	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12680436	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12681841	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13266707	0.84[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs13267765	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13269925	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2326556	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2326557	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2625445	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28495747	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28542403	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28678079	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2875966	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34234629	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34523017	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34775344	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35837434	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35853087	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs592014	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs602724	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603239	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610455	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs621279	0.84[CEU][hapmap]
rs624407	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6471883	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6471884	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs649634	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs664796	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66983460	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs669960	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs677467	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs684573	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6987523	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6991529	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6993237	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6996344	0.95[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7357376	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7462738	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7812421	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7820349	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7822391	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7832964	0.83[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7842105	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9437	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9643524	0.93[EUR][1000 genomes];0.88[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	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	nsv870164	chr8:61484657-61529482	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv6218	chr8:61485410-61530933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1796952	chr8:61492893-61531418	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
7	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs671275	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs671275	RAB2	cis	lesional skin	skin_eQTL
rs671275	LOC643763	cis	parietal	SCAN
rs671275	RAB2	cis	multi-tissue	Pritchard
rs671275	RAB2	cis	uninvolved skin	skin_eQTL
rs671275	RAB2	cis	normal skin	skin_eQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61481000-61527400	Weak transcription	Psoas Muscle	Psoas
2	chr8:61500400-61542200	Weak transcription	Hela-S3	cervix
3	chr8:61506000-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr8:61506400-61532400	Weak transcription	NHLF	lung
5	chr8:61508800-61533000	Weak transcription	HUVEC	blood vessel
6	chr8:61512400-61526200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr8:61512800-61527800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:61513000-61528400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:61515600-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:61515600-61533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr8:61516000-61532000	Weak transcription	NHDF-Ad	bronchial
12	chr8:61516200-61533200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:61517800-61532200	Weak transcription	Small Intestine	intestine
14	chr8:61517800-61537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr8:61518000-61530800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:61518000-61532000	Weak transcription	Colon Smooth Muscle	Colon
17	chr8:61518000-61532000	Weak transcription	Fetal Brain Male	brain
18	chr8:61518000-61534000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr8:61518000-61536600	Weak transcription	Aorta	Aorta
20	chr8:61518200-61526000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:61518200-61526800	Weak transcription	Brain Anterior Caudate	brain
22	chr8:61518200-61527000	Weak transcription	Brain Angular Gyrus	brain
23	chr8:61518200-61530400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr8:61518200-61531000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:61518200-61531400	Weak transcription	Fetal Brain Female	brain
26	chr8:61518200-61532000	Weak transcription	Brain Substantia Nigra	brain
27	chr8:61518200-61532200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr8:61518200-61532200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr8:61518200-61532200	Weak transcription	Fetal Thymus	thymus
30	chr8:61518200-61532200	Weak transcription	Ovary	ovary
31	chr8:61518200-61532200	Weak transcription	Pancreas	Pancrea
32	chr8:61518200-61532800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr8:61518200-61533200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr8:61518200-61533200	Weak transcription	A549	lung
35	chr8:61518200-61535000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr8:61518200-61535600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr8:61518200-61537200	Weak transcription	Gastric	stomach
38	chr8:61518200-61537400	Weak transcription	Spleen	Spleen
39	chr8:61518400-61536400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr8:61519000-61535200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:61519000-61535800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr8:61519200-61527600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr8:61519600-61530400	Weak transcription	Fetal Kidney	kidney
44	chr8:61519800-61541800	Weak transcription	Esophagus	oesophagus
45	chr8:61520200-61540000	Weak transcription	Fetal Intestine Small	intestine
46	chr8:61520400-61526800	Weak transcription	Brain Hippocampus Middle	brain
47	chr8:61520600-61535200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr8:61521200-61528000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr8:61521400-61526000	Strong transcription	Primary hematopoietic stem cells	blood
50	chr8:61521400-61526000	Strong transcription	Muscle Satellite Cultured Cells	--

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