Variant report

Variant	rs13417057
Chromosome Location	chr2:55441565-55441566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55438202..55442828-chr2:55449571..55452245,4	MCF-7	breast:
2	chr2:55275101..55276800-chr2:55441099..55444085,2	K562	blood:
3	chr2:55440554..55442948-chr2:55464620..55466638,2	MCF-7	breast:
4	chr2:55439611..55442389-chr2:55444067..55447159,3	K562	blood:
5	chr2:55439611..55442665-chr2:55443845..55449055,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTIF2-1	chr2:55441523-55442286	ENSG00000203327.2

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000227799	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10172326	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10193022	0.86[AFR][1000 genomes]
rs10197309	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1133181	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1133182	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11679663	0.82[AMR][1000 genomes]
rs11685292	0.82[EUR][1000 genomes]
rs12621144	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13012766	0.82[AMR][1000 genomes]
rs13013134	0.80[AMR][1000 genomes]
rs13019355	0.82[AMR][1000 genomes]
rs13021215	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13023235	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs14026	0.82[AMR][1000 genomes]
rs2864818	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35026006	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35161040	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35890669	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3762509	0.84[ASN][1000 genomes]
rs3935223	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4420737	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4671241	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4671242	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672026	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4672027	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56095114	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6545474	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545475	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545478	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6714830	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6758504	0.84[ASN][1000 genomes]
rs6759911	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7595134	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13417057	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55423800-55448000	Weak transcription	HSMM	muscle
8	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
12	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
14	chr2:55424600-55451200	Weak transcription	HepG2	liver
15	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
19	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:55430000-55443200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
24	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:55432000-55451200	Weak transcription	Dnd41	blood
26	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:55432600-55448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
30	chr2:55433000-55444600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55433000-55448800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:55433000-55448800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
34	chr2:55433000-55450200	Weak transcription	Ovary	ovary
35	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:55433600-55448200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:55433600-55448600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:55437000-55441800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:55441200-55443400	Weak transcription	Brain Substantia Nigra	brain
40	chr2:55441200-55450000	Weak transcription	K562	blood
41	chr2:55441400-55450000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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