Variant report

Variant	rs12991740
Chromosome Location	chr2:172885996-172885997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:172885960-172886373	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172872308..172874513-chr2:172883342..172886066,2	MCF-7	breast:
2	chr2:172884857..172888115-chr2:172946694..172951424,5	K562	blood:
3	chr2:172885280..172887924-chr2:172947289..172951692,6	MCF-7	breast:
4	chr2:172874695..172877681-chr2:172884146..172886439,2	K562	blood:

Variant related genes	Relation type
METAP1D	TF binding region
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1008151	0.86[CEU][hapmap]
rs12052246	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13015360	0.80[EUR][1000 genomes]
rs13020884	0.85[CEU][hapmap]
rs2271758	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs34054371	0.80[EUR][1000 genomes]
rs6433323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6718013	0.89[CEU][hapmap]
rs7584187	0.89[CEU][hapmap]
rs788166	0.86[CEU][hapmap]
rs788170	0.86[CEU][hapmap]
rs788171	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12991740	AC068039.4	cis	Thyroid	GTEx
rs12991740	AC068039.4	cis	Muscle Skeletal	GTEx
rs12991740	AC068039.4	cis	Esophagus Muscularis	GTEx
rs12991740	AC068039.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:172865800-172886400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:172865800-172886600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:172866000-172886800	Weak transcription	HSMMtube	muscle
6	chr2:172874200-172886400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:172878200-172886400	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:172878400-172886000	Weak transcription	HepG2	liver
9	chr2:172878600-172886400	Weak transcription	Ovary	ovary
10	chr2:172878600-172886600	Weak transcription	Psoas Muscle	Psoas
11	chr2:172878600-172898200	Weak transcription	Primary B cells from cord blood	blood
12	chr2:172878800-172886600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:172882000-172886800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:172883400-172886200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:172883400-172886200	Weak transcription	K562	blood
16	chr2:172883600-172886000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:172883800-172886000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:172883800-172887200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:172884200-172886600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:172885200-172886600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:172885400-172886200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:172885600-172886200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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