Variant report

Variant	rs2258180
Chromosome Location	chr2:173686663-173686664
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12477872	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs1344592	0.80[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1863166	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2194720	0.94[ASW][hapmap];0.81[AFR][1000 genomes]
rs2257236	0.89[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2258175	0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468391	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2676512	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2676524	0.91[EUR][1000 genomes]
rs2676525	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2884346	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2258180	DLX2	cis	parietal	SCAN
rs2258180	HOXD4	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173676000-173693400	Weak transcription	Fetal Heart	heart
2	chr2:173679200-173693800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:173679200-173708800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:173685000-173686800	Weak transcription	Brain Angular Gyrus	brain
5	chr2:173686000-173687000	Enhancers	Osteobl	bone
6	chr2:173686000-173687600	Flanking Active TSS	HUVEC	blood vessel
7	chr2:173686000-173687800	Active TSS	Left Ventricle	heart
8	chr2:173686000-173688000	Weak transcription	Fetal Intestine Large	intestine
9	chr2:173686000-173688400	Enhancers	Fetal Thymus	thymus
10	chr2:173686000-173688600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:173686200-173686800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:173686200-173686800	Enhancers	Fetal Stomach	stomach
13	chr2:173686200-173686800	Weak transcription	Psoas Muscle	Psoas
14	chr2:173686200-173687200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:173686400-173687400	Weak transcription	Aorta	Aorta
16	chr2:173686400-173687600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:173686400-173687800	Active TSS	Right Atrium	heart
18	chr2:173686400-173688200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr2:173686400-173690200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:173686600-173686800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:173686600-173686800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:173686600-173686800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr2:173686600-173687000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:173686600-173687000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:173686600-173687200	Active TSS	Adipose Nuclei	Adipose
26	chr2:173686600-173687600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr2:173686600-173687600	Active TSS	Fetal Kidney	kidney
28	chr2:173686600-173687800	Active TSS	Stomach Smooth Muscle	stomach
29	chr2:173686600-173688400	Active TSS	Brain Anterior Caudate	brain
30	chr2:173686600-173689200	Active TSS	Lung	lung
31	chr2:173686600-173690800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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