Variant report

Variant	rs7961081
Chromosome Location	chr12:67060605-67060606
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1480019	1.00[AMR][1000 genomes]
rs17102788	1.00[AMR][1000 genomes]
rs1904540	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2170097	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832449	chr12:66885819-67069953	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv915982	chr12:67050863-67189954	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1047085	chr12:67052384-67199621	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1040203	chr12:67056831-67189837	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv541520	chr12:67056831-67189837	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7961081	BMP4	trans	lymphoblastoid	seeQTL
rs7961081	MEIS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67053000-67062200	Weak transcription	Right Atrium	heart
2	chr12:67056000-67061600	Weak transcription	HSMMtube	muscle
3	chr12:67056800-67061400	Weak transcription	NH-A	brain
4	chr12:67057000-67061800	Weak transcription	HSMM	muscle
5	chr12:67057400-67061400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:67057600-67062000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:67057800-67061600	Weak transcription	HMEC	breast
8	chr12:67057800-67062200	Weak transcription	Pancreas	Pancrea
9	chr12:67058200-67063400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:67059200-67060800	Weak transcription	Fetal Brain Male	brain
11	chr12:67059400-67061200	Weak transcription	Brain Germinal Matrix	brain
12	chr12:67059400-67061400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:67059600-67061400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:67059600-67061400	Weak transcription	Fetal Brain Female	brain
15	chr12:67059600-67062200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:67059800-67061600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:67060000-67062000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:67060400-67061200	Enhancers	Fetal Heart	heart

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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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