Variant report

Variant	rs2838986
Chromosome Location	chr21:47145374-47145375
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	chr21:47143964..47146015-chr21:47147683..47149527,2	K562	blood:
2	chr1:28833935..28836290-chr21:47144062..47146610,2	K562	blood:

Variant related genes	Relation type
ENSG00000200087	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11911413	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8127571	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838986	COL6A1	cis	cerebellum	SCAN
rs2838986	HSF2BP	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47131800-47146200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr21:47135600-47165000	Weak transcription	Primary T cells from cord blood	blood
3	chr21:47141000-47154400	Weak transcription	Thymus	Thymus
4	chr21:47143600-47146200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:47143600-47146400	Enhancers	Fetal Muscle Leg	muscle
6	chr21:47143800-47145600	Enhancers	Fetal Brain Female	brain
7	chr21:47144000-47145800	Enhancers	Fetal Brain Male	brain
8	chr21:47144000-47146000	Weak transcription	Fetal Thymus	thymus
9	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr21:47144400-47145400	Enhancers	Brain Angular Gyrus	brain
11	chr21:47144400-47145600	Enhancers	HSMM	muscle
12	chr21:47144600-47145800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:47144600-47146400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:47144600-47157600	Weak transcription	Right Atrium	heart
15	chr21:47144800-47145400	Enhancers	Brain Substantia Nigra	brain
16	chr21:47144800-47145600	Enhancers	Brain Germinal Matrix	brain
17	chr21:47144800-47145600	Enhancers	HSMMtube	muscle
18	chr21:47144800-47147200	Weak transcription	Adipose Nuclei	Adipose
19	chr21:47145000-47145600	Enhancers	Brain Cingulate Gyrus	brain
20	chr21:47145000-47145800	Enhancers	Brain Hippocampus Middle	brain
21	chr21:47145000-47146600	Enhancers	Spleen	Spleen
22	chr21:47145200-47146000	Enhancers	Fetal Muscle Trunk	muscle
23	chr21:47145200-47147400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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