Variant report

Variant	rs11540309
Chromosome Location	chr10:18969812-18969813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18938885..18940645-chr10:18967631..18969812,2	K562	blood:
2	chr10:18962456..18966517-chr10:18966877..18973376,6	K562	blood:
3	chr10:18969086..18970965-chr10:18973281..18975325,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CACNB2-1	chr10:18967049-18970567	NONHSAT011652

Variant related genes	Relation type
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1027193	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10508562	0.93[CEU][hapmap]
rs10508563	0.87[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1055116	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10741091	0.85[JPT][hapmap]
rs10741111	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10741115	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10741129	0.91[ASN][1000 genomes]
rs10741132	0.92[ASN][1000 genomes]
rs10764582	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs10764601	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10764625	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10764691	0.92[ASN][1000 genomes]
rs10828851	0.90[JPT][hapmap]
rs10828870	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10828871	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs10828896	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10828975	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10829022	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10829037	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10829039	0.81[ASN][1000 genomes]
rs10829058	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10829070	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10829151	0.94[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs10829213	0.92[ASN][1000 genomes]
rs11014981	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs11015196	0.81[ASN][1000 genomes]
rs11015312	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11015435	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11511084	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs11593617	0.81[AMR][1000 genomes]
rs11597737	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11812341	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11812501	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11815228	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12098599	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12359758	0.81[ASN][1000 genomes]
rs12762481	0.93[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12762752	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12765026	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12766105	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12766314	0.93[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs12767046	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12767923	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12768464	0.86[CEU][hapmap]
rs12769425	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12770851	0.93[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs12772009	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12772522	0.93[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs12774519	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12774593	0.91[CEU][hapmap]
rs12778035	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12779018	0.90[EUR][1000 genomes]
rs12779641	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs12779694	0.82[AMR][1000 genomes]
rs12780652	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12781208	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12782882	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12784555	0.93[CEU][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes]
rs12784711	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12784986	0.93[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12785031	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880681	0.93[CEU][hapmap]
rs2130531	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2171922	0.93[CEU][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes]
rs2228645	0.93[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2272274	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs34237250	0.91[AMR][1000 genomes]
rs34359432	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3740102	0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3740104	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3817494	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4237349	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4310518	0.86[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4314963	0.93[CEU][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap]
rs4445544	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4468242	0.93[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4573590	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4575162	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4628589	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4748481	0.82[JPT][hapmap]
rs4748488	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4748496	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748497	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4748498	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748499	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748509	0.92[ASN][1000 genomes]
rs5022622	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs55927700	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57066269	0.81[ASN][1000 genomes]
rs61663155	0.81[AMR][1000 genomes]
rs61842187	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6482515	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6482533	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6482597	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7071300	0.81[AMR][1000 genomes]
rs7072624	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7072963	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7074644	0.81[AMR][1000 genomes]
rs7081461	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7081977	0.81[ASN][1000 genomes]
rs7085318	0.81[AMR][1000 genomes]
rs7087030	0.88[ASN][1000 genomes]
rs7088091	0.90[JPT][hapmap]
rs7089083	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7093454	0.81[AMR][1000 genomes]
rs7096923	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7099260	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7099423	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7100880	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7895784	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7897159	0.93[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7898513	0.83[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs7899017	0.80[ASN][1000 genomes]
rs7904016	0.93[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs7904949	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7905365	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7907891	0.81[AMR][1000 genomes]
rs7909570	0.92[ASN][1000 genomes]
rs7909814	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7909845	0.91[ASN][1000 genomes]
rs7910902	0.88[ASN][1000 genomes]
rs7917584	0.85[JPT][hapmap]
rs7922005	0.81[ASN][1000 genomes]
rs7922550	0.90[JPT][hapmap]
rs7922829	0.90[JPT][hapmap]
rs7923480	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11540309	CACNB2	cis	cerebellum	SCAN
rs11540309	NSUN6	cis	parietal	SCAN
rs11540309	TAAR9	trans	cerebellum	SCAN
rs11540309	FAM188A	cis	cerebellum	SCAN
rs11540309	STAM	cis	parietal	SCAN
rs11540309	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
4	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
6	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
11	chr10:18957400-18971600	Weak transcription	Fetal Heart	heart
12	chr10:18957600-18971200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:18957800-18971000	Weak transcription	Brain Anterior Caudate	brain
14	chr10:18958200-18970000	Weak transcription	HSMMtube	muscle
15	chr10:18959000-18973600	Weak transcription	Left Ventricle	heart
16	chr10:18960000-18972400	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:18960400-18970200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:18960800-18970200	Weak transcription	NHLF	lung
19	chr10:18960800-18973400	Weak transcription	Ovary	ovary
20	chr10:18961000-18970800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:18961000-18973600	Weak transcription	Thymus	Thymus
22	chr10:18961600-18971000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:18961800-18970200	Weak transcription	HMEC	breast
24	chr10:18962400-18973600	Weak transcription	Fetal Intestine Small	intestine
25	chr10:18962400-18973600	Weak transcription	Fetal Stomach	stomach
26	chr10:18963200-18973400	Weak transcription	Pancreas	Pancrea
27	chr10:18963800-18970000	Weak transcription	NHDF-Ad	bronchial
28	chr10:18964000-18972200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:18964000-18973000	Weak transcription	Primary T cells from cord blood	blood
30	chr10:18964200-18973400	Weak transcription	Psoas Muscle	Psoas
31	chr10:18964600-18973600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:18964600-18973800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:18964800-18970000	Weak transcription	A549	lung
34	chr10:18964800-18970400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:18964800-18970800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:18964800-18973400	Weak transcription	Fetal Brain Female	brain
37	chr10:18964800-18973400	Weak transcription	HUVEC	blood vessel
38	chr10:18964800-18973800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr10:18965000-18972800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr10:18965000-18973400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr10:18965200-18970000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr10:18965200-18971600	Weak transcription	Placenta	Placenta
43	chr10:18965200-18972200	Weak transcription	Fetal Muscle Leg	muscle
44	chr10:18965200-18972400	Weak transcription	Colon Smooth Muscle	Colon
45	chr10:18965200-18973400	Weak transcription	Brain Germinal Matrix	brain
46	chr10:18965200-18973400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:18965400-18970000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:18965400-18970000	Weak transcription	GM12878-XiMat	blood
49	chr10:18965400-18973000	Weak transcription	Fetal Thymus	thymus
50	chr10:18965600-18970400	Weak transcription	Primary B cells from peripheral blood	blood

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