Variant report

Variant	rs1025631
Chromosome Location	chr3:87021374-87021375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13087787	0.83[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1436638	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1836918	0.94[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs1898269	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1960268	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2043663	1.00[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2575772	0.80[EUR][1000 genomes]
rs2575775	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs2660777	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2660798	0.89[CEU][hapmap]
rs4859107	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1025631	CHMP2B	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86998800-87036000	Weak transcription	Psoas Muscle	Psoas
2	chr3:87007200-87026600	Weak transcription	Esophagus	oesophagus
3	chr3:87007200-87038400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:87008000-87022600	Weak transcription	HMEC	breast
5	chr3:87008000-87028800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:87008000-87032000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:87008000-87034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:87008200-87022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:87011600-87022600	Weak transcription	HUVEC	blood vessel
10	chr3:87011600-87026600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:87012600-87032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:87012800-87022200	Strong transcription	NH-A	brain
13	chr3:87015000-87028400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:87015400-87027200	Weak transcription	Hela-S3	cervix
15	chr3:87016200-87039000	Weak transcription	Fetal Stomach	stomach
16	chr3:87016800-87021800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr3:87016800-87036800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:87017000-87022000	Strong transcription	HSMM	muscle
19	chr3:87017000-87029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:87017600-87039000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:87018200-87022800	Weak transcription	Gastric	stomach
22	chr3:87018200-87026800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:87018200-87032600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:87018200-87033600	Weak transcription	A549	lung
25	chr3:87018400-87023000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:87018400-87036400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:87018600-87023400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:87018600-87026400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:87018600-87026400	Weak transcription	Aorta	Aorta
30	chr3:87018600-87026600	Weak transcription	Pancreas	Pancrea
31	chr3:87018600-87034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:87019000-87025600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:87019200-87025200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:87019400-87021800	Strong transcription	Osteobl	bone
35	chr3:87019400-87026200	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:87019400-87036600	Weak transcription	Fetal Brain Male	brain
37	chr3:87019600-87022600	Weak transcription	Fetal Lung	lung
38	chr3:87019800-87022000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:87019800-87022600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:87019800-87026400	Weak transcription	Ovary	ovary
41	chr3:87020000-87022800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:87020000-87024400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:87020000-87026400	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:87020200-87021800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:87020400-87027200	Genic enhancers	NHDF-Ad	bronchial
46	chr3:87020600-87021800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:87020600-87022400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:87020600-87022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:87020800-87023400	Weak transcription	NHLF	lung
50	chr3:87021200-87021600	Strong transcription	Placenta	Placenta

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