Variant report

Variant	rs13013988
Chromosome Location	chr2:172917076-172917077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172915830..172918019-chr2:172965851..172967372,2	MCF-7	breast:
2	chr2:172866585..172869561-chr2:172915980..172919427,3	K562	blood:
3	chr2:172915629..172918406-chr2:172934350..172936344,2	MCF-7	breast:
4	chr2:172863680..172867220-chr2:172914121..172918663,4	MCF-7	breast:
5	chr2:172915456..172917874-chr2:172919849..172921461,2	MCF-7	breast:
6	chr2:172909159..172912131-chr2:172917033..172919851,3	MCF-7	breast:
7	chr2:172872127..172874571-chr2:172915848..172917626,2	MCF-7	breast:
8	chr2:172915241..172921806-chr2:172947514..172951783,14	MCF-7	breast:
9	chr2:172916809..172918657-chr2:172945564..172947082,2	MCF-7	breast:
10	chr2:172916439..172918437-chr2:172924109..172926008,2	K562	blood:
11	chr2:172910524..172912386-chr2:172915560..172917116,2	K562	blood:
12	chr2:172901921..172905424-chr2:172916575..172920187,5	MCF-7	breast:
13	chr2:172914458..172918465-chr2:172959410..172965426,7	MCF-7	breast:
14	chr2:172914690..172917285-chr2:172958653..172961540,2	MCF-7	breast:
15	chr2:172909670..172912609-chr2:172916665..172919120,2	MCF-7	breast:
16	chr2:172901732..172906441-chr2:172911766..172917938,8	K562	blood:
17	chr2:172915810..172921925-chr2:172947139..172950933,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11681005	0.87[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs11688839	0.87[CEU][hapmap];0.80[YRI][hapmap]
rs12996935	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs17500199	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1965159	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72892894	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	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
2	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
3	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
4	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13013988	B3GALT1	cis	cerebellum	SCAN
rs13013988	SLC25A12	cis	cerebellum	SCAN
rs13013988	SLC25A12	cis	parietal	SCAN
rs13013988	MAP1D	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911000-172930000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172911200-172947200	Weak transcription	HSMM	muscle
3	chr2:172913400-172917200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
5	chr2:172914800-172918000	Enhancers	K562	blood
6	chr2:172914800-172918600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:172915200-172917400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:172916000-172917800	Enhancers	Fetal Lung	lung
9	chr2:172916000-172918600	Enhancers	Fetal Kidney	kidney
10	chr2:172916200-172917200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:172916200-172917400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:172916200-172917400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:172916200-172917600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:172916200-172917800	Enhancers	Ovary	ovary
15	chr2:172916200-172918400	Enhancers	Brain Germinal Matrix	brain
16	chr2:172916400-172917200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:172916400-172917400	Enhancers	HUVEC	blood vessel
18	chr2:172916400-172917600	Enhancers	Hela-S3	cervix
19	chr2:172916400-172918000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:172916400-172918600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:172916600-172917200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:172916600-172917600	Flanking Active TSS	HepG2	liver
23	chr2:172916600-172917800	Enhancers	Brain Substantia Nigra	brain
24	chr2:172916800-172917200	Flanking Active TSS	Liver	Liver
25	chr2:172916800-172917200	Enhancers	Brain Anterior Caudate	brain
26	chr2:172916800-172917200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:172916800-172917200	Enhancers	A549	lung
28	chr2:172916800-172917400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:172916800-172917600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:172916800-172917600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:172916800-172917600	Enhancers	NHLF	lung
32	chr2:172916800-172917800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:172916800-172917800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr2:172917000-172917400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:172917000-172917400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:172917000-172917400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:172917000-172917400	Enhancers	Brain Angular Gyrus	brain
38	chr2:172917000-172917400	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:172917000-172917400	Active TSS	Fetal Brain Male	brain
40	chr2:172917000-172917400	Flanking Active TSS	Osteobl	bone
41	chr2:172917000-172917600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:172917000-172917800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:172917000-172918000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:172917000-172918000	Enhancers	HUES6 Cell Line	embryonic stem cell

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