Variant report

Variant	rs3771341
Chromosome Location	chr2:234673239-234673240
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10178992	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10929302	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11673726	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11695484	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11888459	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11891311	0.90[ASN][1000 genomes]
rs12987866	0.80[EUR][1000 genomes]
rs13401281	0.87[ASN][1000 genomes]
rs13410335	0.87[ASN][1000 genomes]
rs17862875	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17864701	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1983023	0.90[ASN][1000 genomes]
rs2018985	0.92[ASN][1000 genomes]
rs2885296	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34352510	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4148324	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4148325	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341922	0.81[ASN][1000 genomes]
rs4477910	0.90[ASN][1000 genomes]
rs6431625	0.82[ASN][1000 genomes]
rs6714634	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6722076	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6742078	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744284	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747843	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564935	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7567468	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7604115	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs887829	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929596	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv1811811	chr2:234633964-234709430	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3771341	EFHD1	cis	cerebellum	SCAN
rs3771341	SP100	cis	cerebellum	SCAN
rs3771341	NPPC	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234666800-234673600	Weak transcription	Colonic Mucosa	Colon
2	chr2:234667200-234673800	Enhancers	Stomach Mucosa	stomach
3	chr2:234669200-234683800	Weak transcription	Gastric	stomach
4	chr2:234671400-234675200	Enhancers	Fetal Intestine Small	intestine
5	chr2:234672000-234673600	Active TSS	Duodenum Mucosa	Duodenum
6	chr2:234672000-234673800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:234672000-234673800	Enhancers	A549	lung
8	chr2:234672000-234675200	Enhancers	Fetal Intestine Large	intestine
9	chr2:234672400-234673400	Enhancers	HSMM	muscle
10	chr2:234672400-234673600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:234672400-234673600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr2:234672400-234673800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:234672400-234673800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:234672400-234673800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:234672400-234673800	Enhancers	HMEC	breast
16	chr2:234672600-234673600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:234672600-234673600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:234672600-234673800	Enhancers	NHLF	lung
19	chr2:234672800-234673400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:234672800-234673400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:234672800-234673800	Enhancers	NH-A	brain
22	chr2:234672800-234685400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:234673000-234673400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:234673000-234673600	Bivalent Enhancer	Small Intestine	intestine
25	chr2:234673200-234673600	Flanking Active TSS	Osteobl	bone
26	chr2:234673200-234673800	Flanking Active TSS	Liver	Liver
27	chr2:234673200-234673800	Enhancers	NHEK	skin
28	chr2:234673200-234674600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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