Variant report

Variant	rs2946154
Chromosome Location	chr8:61488859-61488860
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	chr8:61441838..61443527-chr8:61486659..61489457,2	MCF-7	breast:
2	chr8:61486393..61488900-chr8:61501099..61503900,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CA8-11	chr8:61488669-61488931	ucscGeneNc_uc003xuc_1

Extended variants
information (count: 129 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10096140	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098769	0.92[CEU][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10102740	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10106752	1.00[YRI][hapmap]
rs1017861	1.00[YRI][hapmap]
rs1017862	1.00[YRI][hapmap]
rs10435601	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10808709	0.89[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10808710	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957142	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957144	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957145	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957147	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957150	0.92[CEU][hapmap]
rs10957151	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1120591	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11774081	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11776939	0.81[EUR][1000 genomes]
rs11777673	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11777706	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11995549	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11996592	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678742	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12680437	1.00[YRI][hapmap]
rs12680781	0.89[EUR][1000 genomes]
rs12681129	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319104	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319105	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13257359	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13262390	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265543	0.87[EUR][1000 genomes]
rs13276831	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13439252	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1552071	0.80[EUR][1000 genomes]
rs17814894	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs1842389	0.81[EUR][1000 genomes]
rs1893272	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1941463	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013112	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2056415	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096890	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2155829	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186986	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272620	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272621	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326560	0.93[CEU][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326561	0.93[CEU][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326562	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326568	0.93[CEU][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326569	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326570	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2326571	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2625441	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625446	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2680297	1.00[YRI][hapmap]
rs28649594	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875967	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875968	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875973	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875974	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930040	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2981277	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735825	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735826	0.92[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3929643	0.88[EUR][1000 genomes]
rs41420549	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288413	1.00[YRI][hapmap]
rs4403445	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4452821	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4738813	1.00[YRI][hapmap]
rs4738816	1.00[YRI][hapmap]
rs4738817	1.00[YRI][hapmap]
rs55825491	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56294255	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586377	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs595255	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600811	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603035	0.93[CEU][hapmap]
rs608401	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615031	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs617834	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625850	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629268	0.92[CEU][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs631408	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6471885	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6471886	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471888	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652422	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659118	0.88[EUR][1000 genomes]
rs660865	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs669599	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs671204	1.00[YRI][hapmap]
rs67420552	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684066	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs687978	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6984378	0.96[CEU][hapmap]
rs6987084	0.93[CEU][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6992869	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6993019	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6995041	0.93[CEU][hapmap]
rs6995515	0.89[CEU][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7000166	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001696	0.87[EUR][1000 genomes]
rs7007434	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7012181	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7013249	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7815543	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7822169	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7822621	1.00[YRI][hapmap]
rs7824045	0.93[CEU][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7825612	0.81[EUR][1000 genomes]
rs7827453	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7829359	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7830710	0.80[EUR][1000 genomes]
rs7834395	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7839474	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7839516	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7842586	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs876957	1.00[YRI][hapmap]
rs900503	1.00[YRI][hapmap]
rs900504	1.00[YRI][hapmap]
rs9298039	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948422	0.87[EUR][1000 genomes]
rs9643523	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2946154	RP11-163N6.2	cis	Thyroid	GTEx
rs2946154	RAB2A	cis	Thyroid	GTEx
rs2946154	RAB2	cis	uninvolved skin	skin_eQTL
rs2946154	RAB2	cis	normal skin	skin_eQTL
rs2946154	RAB2	cis	lesional skin	skin_eQTL
rs2946154	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs2946154	RAB2A	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61439400-61494600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:61448600-61505400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:61458200-61497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:61459400-61495800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr8:61466400-61516800	Weak transcription	Stomach Mucosa	stomach
6	chr8:61467200-61515400	Weak transcription	Fetal Brain Male	brain
7	chr8:61469000-61495000	Weak transcription	Brain Germinal Matrix	brain
8	chr8:61473200-61489200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:61473600-61493800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:61473600-61495000	Weak transcription	Spleen	Spleen
11	chr8:61473600-61497800	Weak transcription	Lung	lung
12	chr8:61474200-61504000	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:61474600-61496200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:61474600-61496400	Weak transcription	Thymus	Thymus
15	chr8:61474800-61496000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:61474800-61504000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr8:61475000-61493600	Weak transcription	Fetal Kidney	kidney
18	chr8:61475000-61495600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:61475400-61494600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr8:61475400-61498200	Weak transcription	A549	lung
21	chr8:61476200-61495400	Weak transcription	Hela-S3	cervix
22	chr8:61476200-61504800	Weak transcription	NHLF	lung
23	chr8:61476200-61517000	Weak transcription	Brain Angular Gyrus	brain
24	chr8:61476400-61495400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr8:61476400-61496400	Weak transcription	Brain Substantia Nigra	brain
26	chr8:61476600-61495400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr8:61476800-61495200	Weak transcription	Brain Anterior Caudate	brain
28	chr8:61477000-61495000	Weak transcription	Ovary	ovary
29	chr8:61477200-61491200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr8:61477200-61494600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr8:61477400-61497600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr8:61477800-61493600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr8:61477800-61496400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr8:61480000-61491200	Strong transcription	Primary B cells from cord blood	blood
35	chr8:61480800-61496600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr8:61481000-61496800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr8:61481000-61497800	Weak transcription	Gastric	stomach
38	chr8:61481000-61527400	Weak transcription	Psoas Muscle	Psoas
39	chr8:61481200-61504200	Weak transcription	HMEC	breast
40	chr8:61481400-61489200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr8:61482200-61496200	Weak transcription	Brain Hippocampus Middle	brain
42	chr8:61482400-61489200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr8:61482800-61490600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:61482800-61491800	Weak transcription	Fetal Intestine Small	intestine
45	chr8:61482800-61496400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr8:61482800-61498000	Weak transcription	Aorta	Aorta
47	chr8:61482800-61504000	Weak transcription	HSMMtube	muscle
48	chr8:61482800-61505800	Weak transcription	Esophagus	oesophagus
49	chr8:61483000-61489000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:61483000-61495000	Weak transcription	Pancreas	Pancrea

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