Variant report

Variant	rs12141923
Chromosome Location	chr1:210860558-210860559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10494928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119571	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11119575	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12122565	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12123159	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12125545	0.85[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs12126038	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12127398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140954	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17188416	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17188506	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2226023	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs2357921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28513183	0.82[EUR][1000 genomes]
rs4628571	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs60195529	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873150	chr1:210808270-210893233	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv468083	chr1:210854815-210876192	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv549123	chr1:210854815-210876192	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12141923	G0S2	cis	cerebellum	SCAN
rs12141923	C1orf107	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210835400-210863200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:210838000-210880400	Weak transcription	Gastric	stomach
3	chr1:210845400-210866000	Weak transcription	Spleen	Spleen
4	chr1:210846000-210865600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:210846200-210862400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:210846200-210865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:210846400-210884600	Weak transcription	Ovary	ovary
8	chr1:210847600-210862200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:210855800-210861800	Weak transcription	Brain Anterior Caudate	brain
10	chr1:210856000-210860600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:210856000-210863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:210856200-210862000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:210856200-210864200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:210857000-210864800	Weak transcription	Fetal Stomach	stomach
15	chr1:210857200-210882600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:210857400-210864000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:210857800-210863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:210857800-210870800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:210858000-210864800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:210858000-210880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:210859400-210860800	Enhancers	Liver	Liver
22	chr1:210859800-210862600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:210859800-210863800	Enhancers	HSMM	muscle
24	chr1:210859800-210865600	Weak transcription	GM12878-XiMat	blood
25	chr1:210860000-210863800	Enhancers	A549	lung
26	chr1:210860000-210863800	Enhancers	Osteobl	bone
27	chr1:210860200-210861600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:210860400-210860800	Enhancers	NHLF	lung
29	chr1:210860400-210861000	Flanking Active TSS	HSMMtube	muscle
30	chr1:210860400-210862800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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