Variant report

Variant	rs1388256
Chromosome Location	chr3:56627048-56627049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATA12-5	chr3:56626998-56627089	NONHSAT090054

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10222629	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054092	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1054093	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865997	0.81[MEX][hapmap]
rs11130525	1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130527	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11712664	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712799	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11719707	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719726	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12486047	0.81[MEX][hapmap]
rs13075010	0.83[CHB][hapmap]
rs1316647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13317989	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565378	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17216657	0.82[CHB][hapmap]
rs17216685	0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17216747	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs17288852	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs1812347	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1873256	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291498	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291500	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2317132	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282524	0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs282525	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282526	0.81[AMR][1000 genomes]
rs282530	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282531	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282542	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3172355	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3732505	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4681726	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681736	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681738	0.82[ASN][1000 genomes]
rs4681903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681904	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4681937	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681955	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682001	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682002	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974221	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974223	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974225	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs55742226	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55828519	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55865922	0.81[ASN][1000 genomes]
rs56126040	0.81[ASN][1000 genomes]
rs56172256	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56263252	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56356916	0.87[ASN][1000 genomes]
rs62251234	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62255964	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445811	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445812	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6764730	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767903	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769055	0.81[MEX][hapmap]
rs6794450	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799086	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612464	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7620896	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628343	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633478	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641898	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645941	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7647095	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7648297	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649872	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs873840	0.82[CEU][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9311609	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311612	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs953540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809117	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814014	0.95[JPT][hapmap]
rs9816100	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816265	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819952	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826788	0.94[ASN][1000 genomes]
rs9830377	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834064	0.81[MEX][hapmap]
rs9834239	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835134	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9841851	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847362	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861577	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864701	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867302	0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868059	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871265	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872059	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881152	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9883842	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv528087	chr3:56608033-56628031	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1388256	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs1388256	CCDC66	cis	lymphoblastoid	seeQTL
rs1388256	CCDC66	cis	multi-tissue	Pritchard
rs1388256	FLNB	cis	cerebellum	SCAN
rs1388256	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
2	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
3	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
4	chr3:56600600-56640000	Weak transcription	NHLF	lung
5	chr3:56603000-56631600	Weak transcription	Fetal Brain Male	brain
6	chr3:56603200-56650400	Weak transcription	K562	blood
7	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:56604200-56627600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:56604600-56627600	Weak transcription	HUVEC	blood vessel
10	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
11	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
12	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
13	chr3:56606000-56627600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:56606000-56627600	Weak transcription	Left Ventricle	heart
15	chr3:56606000-56629200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
17	chr3:56606600-56627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:56606800-56627600	Weak transcription	Osteobl	bone
19	chr3:56607600-56627200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:56607800-56627400	Weak transcription	Brain Anterior Caudate	brain
21	chr3:56607800-56627600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:56607800-56627600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:56607800-56627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:56607800-56627600	Weak transcription	NHDF-Ad	bronchial
25	chr3:56607800-56627800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:56607800-56629800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
28	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
29	chr3:56608200-56627600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:56609400-56638600	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:56610000-56627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:56610000-56627600	Weak transcription	HSMM	muscle
33	chr3:56616200-56633800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:56616400-56639400	Weak transcription	Lung	lung
35	chr3:56617200-56627200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:56617200-56627400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:56617200-56627600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:56617200-56627600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:56617200-56629000	Weak transcription	Fetal Brain Female	brain
40	chr3:56617200-56629400	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:56617200-56629400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:56617200-56629800	Weak transcription	Hela-S3	cervix
43	chr3:56617200-56630000	Weak transcription	Fetal Stomach	stomach
44	chr3:56617200-56639200	Weak transcription	Thymus	Thymus
45	chr3:56617200-56639600	Weak transcription	Aorta	Aorta
46	chr3:56617400-56627200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:56617400-56627400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:56617400-56627400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:56617400-56627400	Weak transcription	GM12878-XiMat	blood
50	chr3:56617400-56627600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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