Variant report

Variant	rs11062161
Chromosome Location	chr12:2329970-2329971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCP1B-2	chr12:2329703-2330020	ENSG00000256025.1
2	lnc-DCP1B-2	chr12:2329448-2330020	NONHSAT025448
3	lnc-DCP1B-2	chr12:2329703-2330020	NONHSAT025449

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1006737	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs1016388	0.89[CEU][hapmap]
rs10774034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774035	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10848642	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062159	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062162	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062166	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062170	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1108073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108074	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108075	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108221	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315711	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12424245	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2159100	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2190771	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239030	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2239033	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2283291	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3794297	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3922316	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765904	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765905	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs6489353	0.82[CEU][hapmap]
rs758170	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs769087	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7965923	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11062161	CACNA1C	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2320400-2335800	Weak transcription	NHLF	lung
2	chr12:2320800-2331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:2323200-2340200	Enhancers	Fetal Heart	heart
4	chr12:2323600-2336000	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:2323800-2338800	Weak transcription	Spleen	Spleen
6	chr12:2325400-2330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:2325800-2334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:2326000-2334600	Weak transcription	Osteobl	bone
9	chr12:2326600-2330800	Enhancers	Left Ventricle	heart
10	chr12:2327200-2336200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:2328400-2330600	Enhancers	Right Ventricle	heart
12	chr12:2328600-2334200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:2328800-2333600	Weak transcription	Fetal Lung	lung
14	chr12:2329000-2330600	Enhancers	Colon Smooth Muscle	Colon
15	chr12:2329200-2330400	Enhancers	Rectal Smooth Muscle	rectum
16	chr12:2329800-2330600	Enhancers	Stomach Smooth Muscle	stomach
17	chr12:2329800-2330800	Enhancers	Aorta	Aorta
18	chr12:2329800-2338800	Weak transcription	Right Atrium	heart

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