Variant report

Variant	rs2107944
Chromosome Location	chr7:141053519-141053520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10229879	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10245819	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10253128	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10274567	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859575	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55728485	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55996608	0.88[ASN][1000 genomes]
rs56216313	0.82[ASN][1000 genomes]
rs6946712	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6964699	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6965337	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6978289	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779102	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv831160	chr7:141009011-141188046	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3428582	chr7:141013551-141064197	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv34135	chr7:141047454-141492898	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2107944	CLCN1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:141037200-141054200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:141041200-141053600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:141047600-141054200	Weak transcription	Right Atrium	heart
4	chr7:141047600-141054800	Weak transcription	Left Ventricle	heart
5	chr7:141049400-141054200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:141049600-141054200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:141049800-141054400	Weak transcription	Brain Germinal Matrix	brain
8	chr7:141049800-141054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:141051400-141054200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:141051400-141055000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:141051800-141053800	Weak transcription	Right Ventricle	heart
12	chr7:141052800-141055800	Enhancers	Brain Cingulate Gyrus	brain
13	chr7:141053000-141055400	Enhancers	Brain Anterior Caudate	brain
14	chr7:141053000-141055400	Enhancers	Brain Hippocampus Middle	brain
15	chr7:141053000-141059600	Enhancers	Fetal Lung	lung
16	chr7:141053200-141053600	Weak transcription	Brain Angular Gyrus	brain
17	chr7:141053200-141054200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:141053200-141054200	Weak transcription	Fetal Brain Male	brain
19	chr7:141053200-141054400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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