Variant report

Variant	rs723042
Chromosome Location	chr2:33541702-33541703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10189109	0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10191688	0.95[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11684935	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1453842	0.82[CHD][hapmap]
rs2276591	0.86[CHB][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4569454	0.85[CHB][hapmap]
rs6737863	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7580131	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs817531	0.84[GIH][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs723042	SPAST	cis	parietal	SCAN
rs723042	CRIM1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33517200-33545000	Weak transcription	Fetal Kidney	kidney
3	chr2:33517200-33545800	Weak transcription	Fetal Lung	lung
4	chr2:33517200-33546400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:33517800-33543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:33523400-33545200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:33523600-33546200	Weak transcription	K562	blood
8	chr2:33523800-33550600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:33524200-33546600	Weak transcription	Small Intestine	intestine
10	chr2:33529600-33546400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:33529800-33546600	Weak transcription	Psoas Muscle	Psoas
12	chr2:33529800-33561000	Weak transcription	HUVEC	blood vessel
13	chr2:33529800-33609400	Weak transcription	Right Ventricle	heart
14	chr2:33530000-33543000	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:33533400-33542800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:33535600-33544600	Weak transcription	NHLF	lung
17	chr2:33537400-33545800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:33538400-33541800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:33538400-33543200	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr2:33538400-33545600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:33538400-33545800	Strong transcription	Osteobl	bone
22	chr2:33538600-33541800	Weak transcription	NHDF-Ad	bronchial
23	chr2:33538800-33542600	Weak transcription	Ovary	ovary
24	chr2:33539000-33542600	Weak transcription	Lung	lung
25	chr2:33539000-33544800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:33539400-33542000	Weak transcription	Esophagus	oesophagus
27	chr2:33539400-33542600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:33539600-33545600	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:33539800-33543600	Strong transcription	NH-A	brain
30	chr2:33540400-33542000	Strong transcription	Liver	Liver
31	chr2:33540400-33543600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:33540800-33580800	Weak transcription	Placenta	Placenta
33	chr2:33541000-33542600	Weak transcription	Left Ventricle	heart
34	chr2:33541000-33542600	Weak transcription	Right Atrium	heart
35	chr2:33541000-33543000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:33541000-33544000	Weak transcription	Fetal Stomach	stomach
37	chr2:33541000-33546400	Weak transcription	Aorta	Aorta
38	chr2:33541000-33547000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:33541200-33542400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:33541200-33542600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:33541200-33547200	Weak transcription	Gastric	stomach
42	chr2:33541400-33541800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:33541600-33541800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:33541600-33543600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:33541600-33543600	Enhancers	Fetal Heart	heart

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