Variant report

Variant	rs4712899
Chromosome Location	chr6:25226272-25226273
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	chr6:25225956..25229014-chr6:25230558..25232787,3	K562	blood:
2	chr6:25218882..25222296-chr6:25222360..25226467,5	K562	blood:

Variant related genes	Relation type
ENSG00000219681	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2328876	0.92[ASN][1000 genomes]
rs4712900	0.92[ASN][1000 genomes]
rs7769912	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv883483	chr6:25200842-25272435	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4712899	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs4712899	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25221400-25229200	Weak transcription	Placenta	Placenta
2	chr6:25221400-25229400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:25223800-25229200	Weak transcription	HSMMtube	muscle
4	chr6:25224200-25227600	Weak transcription	Fetal Intestine Large	intestine
5	chr6:25224200-25229000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:25224200-25229000	Weak transcription	NHLF	lung
7	chr6:25224200-25229200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:25224200-25229200	Weak transcription	HSMM	muscle
9	chr6:25224200-25229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:25224400-25229200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:25224400-25229200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:25224400-25229200	Weak transcription	Hela-S3	cervix
13	chr6:25224400-25229200	Weak transcription	NHDF-Ad	bronchial
14	chr6:25224400-25229400	Weak transcription	HMEC	breast
15	chr6:25224400-25229400	Weak transcription	Osteobl	bone
16	chr6:25224400-25230000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:25224600-25229200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:25224600-25229200	Weak transcription	NH-A	brain
19	chr6:25224800-25229400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:25225000-25227000	Weak transcription	Thymus	Thymus

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