Variant report

Variant	rs2971542
Chromosome Location	chr3:141345102-141345103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141337365..141343869-chr3:141344227..141348794,9	K562	blood:
2	chr3:141344934..141347030-chr3:141358252..141360614,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1011330	0.85[ASN][1000 genomes]
rs10935431	0.84[JPT][hapmap]
rs11711597	0.86[ASN][1000 genomes]
rs12632759	0.86[JPT][hapmap]
rs13089727	0.84[JPT][hapmap]
rs1400685	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1994845	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2131495	0.95[ASN][1000 genomes]
rs2172472	0.83[ASN][1000 genomes]
rs2176410	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2249481	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2640004	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2640006	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2640007	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2640008	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2640019	0.93[CHB][hapmap];0.95[JPT][hapmap]
rs2677420	0.81[ASN][1000 genomes]
rs295294	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs295296	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs295315	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs295317	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2971538	0.94[ASN][1000 genomes]
rs2971540	0.83[ASN][1000 genomes]
rs4467426	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs4683407	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs6440024	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs6768509	0.84[JPT][hapmap]
rs6784270	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs6784413	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs6791890	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6805124	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7618625	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7639695	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7650897	0.84[JPT][hapmap]
rs868767	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs868768	0.84[CHD][hapmap];0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	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
rs2971542	CLSTN2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141332400-141345800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:141342600-141346000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:141344000-141345800	Enhancers	HMEC	breast
4	chr3:141344200-141345200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:141344200-141345800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:141344200-141345800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:141344200-141346600	Enhancers	Ovary	ovary
8	chr3:141344400-141346000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:141344600-141345600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:141345000-141345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:141345000-141346600	Weak transcription	Fetal Intestine Large	intestine

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