Variant report

Variant	rs12680436
Chromosome Location	chr8:61511725-61511726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61511100..61513643-chr8:61515847..61518764,3	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10091703	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10100740	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101576	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10101714	0.88[ASN][1000 genomes]
rs10103438	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10109278	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110436	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014860	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435602	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957136	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957137	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10957138	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957140	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957141	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957143	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10957146	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957149	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774500	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778708	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778772	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778888	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782178	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782463	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11784284	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11786146	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11988528	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678694	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681841	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266707	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13267765	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13267828	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13269925	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480342	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2625445	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28495747	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542403	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28678079	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2875966	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234629	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523017	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775344	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35837434	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35853087	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592014	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602724	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603239	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610455	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624407	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471884	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs649634	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664796	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66983460	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs671275	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs677467	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684573	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987523	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991529	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6993237	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996344	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998294	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7357376	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462738	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812421	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7820349	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7822391	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7832664	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7832964	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7842105	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9437	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643524	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12680436	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs12680436	RAB2A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61466400-61516800	Weak transcription	Stomach Mucosa	stomach
2	chr8:61467200-61515400	Weak transcription	Fetal Brain Male	brain
3	chr8:61476200-61517000	Weak transcription	Brain Angular Gyrus	brain
4	chr8:61481000-61527400	Weak transcription	Psoas Muscle	Psoas
5	chr8:61483800-61515800	Weak transcription	Colonic Mucosa	Colon
6	chr8:61485400-61515400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:61489400-61514000	Weak transcription	Right Ventricle	heart
8	chr8:61491400-61517000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:61493600-61518000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr8:61495600-61516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:61495600-61517000	Weak transcription	Pancreas	Pancrea
12	chr8:61495600-61517200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:61495600-61517600	Weak transcription	Spleen	Spleen
14	chr8:61496400-61515400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr8:61496600-61515000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr8:61496800-61515200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:61496800-61517200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:61497000-61511800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:61497400-61512000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr8:61498200-61517200	Weak transcription	Gastric	stomach
21	chr8:61499400-61516600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:61499600-61514000	Weak transcription	Fetal Stomach	stomach
23	chr8:61500400-61542200	Weak transcription	Hela-S3	cervix
24	chr8:61501200-61512200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr8:61503400-61517200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr8:61504000-61517000	Strong transcription	Fetal Thymus	thymus
27	chr8:61504400-61516600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr8:61504400-61517200	Strong transcription	Adipose Nuclei	Adipose
29	chr8:61504800-61515400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr8:61505600-61515200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr8:61506000-61516800	Weak transcription	Small Intestine	intestine
32	chr8:61506000-61517000	Weak transcription	Esophagus	oesophagus
33	chr8:61506000-61523200	Weak transcription	Fetal Heart	heart
34	chr8:61506000-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:61506200-61514400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr8:61506200-61515200	Weak transcription	K562	blood
37	chr8:61506200-61516200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:61506200-61517200	Weak transcription	Aorta	Aorta
39	chr8:61506200-61517200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr8:61506400-61512800	Weak transcription	Brain Substantia Nigra	brain
41	chr8:61506400-61514000	Weak transcription	HepG2	liver
42	chr8:61506400-61532400	Weak transcription	NHLF	lung
43	chr8:61506600-61517400	Weak transcription	Brain Anterior Caudate	brain
44	chr8:61506800-61515200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr8:61506800-61515200	Weak transcription	HMEC	breast
46	chr8:61506800-61517600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr8:61506800-61517600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr8:61507000-61512000	Weak transcription	NH-A	brain
49	chr8:61507000-61515200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr8:61507000-61515400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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