Variant report

Variant	rs386965
Chromosome Location	chr16:79652541-79652542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1019527	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs374480	0.83[ASN][1000 genomes]
rs410059	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6564681	0.84[AFR][1000 genomes]
rs7188272	0.82[AFR][1000 genomes]
rs7196953	0.80[AFR][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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv833295	chr16:79568878-79726768	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	21833088	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs386965	LDHD	cis	cerebellum	SCAN
rs386965	KARS	cis	cerebellum	SCAN
rs386965	BCAR1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79636200-79653800	Weak transcription	Right Atrium	heart
2	chr16:79650600-79653400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr16:79650800-79652800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr16:79650800-79653400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr16:79651000-79652800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr16:79651000-79653600	Enhancers	Dnd41	blood
7	chr16:79651200-79652600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:79651200-79652800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:79651200-79653400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr16:79651600-79653400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr16:79651600-79653400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:79651600-79653600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:79651800-79652600	Enhancers	Primary hematopoietic stem cells	blood
14	chr16:79651800-79652600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:79651800-79652800	Enhancers	Fetal Thymus	thymus
16	chr16:79651800-79653000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr16:79652000-79652600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr16:79652000-79653400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr16:79652200-79652600	Enhancers	Primary T cells from cord blood	blood
20	chr16:79652200-79652600	Enhancers	HSMMtube	muscle
21	chr16:79652200-79653000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr16:79652200-79653400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr16:79652400-79652800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr16:79652400-79652800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:79652400-79652800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:79652400-79652800	Enhancers	Fetal Muscle Trunk	muscle
27	chr16:79652400-79652800	Enhancers	Fetal Muscle Leg	muscle
28	chr16:79652400-79652800	Enhancers	Placenta	Placenta
29	chr16:79652400-79652800	Enhancers	Spleen	Spleen

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