Variant report

Variant	rs1135317
Chromosome Location	chr1:210857457-210857458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10863850	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119569	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126648	0.95[ASN][1000 genomes]
rs1890841	0.95[ASN][1000 genomes]
rs1934615	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1934616	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3135473	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4472816	0.84[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1135317	NFASC	cis	parietal	SCAN

Chromatin state (count:31 , 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	chr1:210837800-210859800	Weak transcription	Right Ventricle	heart
3	chr1:210838000-210880400	Weak transcription	Gastric	stomach
4	chr1:210845400-210866000	Weak transcription	Spleen	Spleen
5	chr1:210845800-210857600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:210846000-210865600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:210846200-210862400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:210846200-210865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:210846400-210884600	Weak transcription	Ovary	ovary
10	chr1:210847000-210860200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:210847600-210862200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:210852200-210857800	Strong transcription	HSMMtube	muscle
13	chr1:210852600-210857800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:210852800-210860400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:210853400-210857800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:210854200-210858000	Enhancers	Fetal Muscle Leg	muscle
17	chr1:210855200-210859400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:210855400-210858800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:210855800-210861800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:210856000-210860600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:210856000-210863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:210856200-210862000	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:210856200-210864200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:210857000-210859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:210857000-210859800	Weak transcription	HSMM	muscle
26	chr1:210857000-210864800	Weak transcription	Fetal Stomach	stomach
27	chr1:210857200-210858000	Enhancers	GM12878-XiMat	blood
28	chr1:210857200-210882600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:210857400-210857600	Weak transcription	Pancreas	Pancrea
30	chr1:210857400-210859600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:210857400-210864000	Weak transcription	Fetal Muscle Trunk	muscle

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