Variant report

Variant	rs6414015
Chromosome Location	chr2:134513100-134513101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1110673	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472557	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12474261	0.83[ASN][1000 genomes]
rs1348838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374401	0.84[ASN][1000 genomes]
rs1596918	0.83[ASN][1000 genomes]
rs2321203	0.83[ASN][1000 genomes]
rs2321298	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2321301	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3936142	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4056124	0.83[ASN][1000 genomes]
rs4270397	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4343520	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4467329	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4505578	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547575	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4549152	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4553871	0.83[ASN][1000 genomes]
rs4558640	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4560170	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6430446	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6430447	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6430452	0.83[ASN][1000 genomes]
rs6711922	0.80[ASN][1000 genomes]
rs6726492	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6743076	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6745752	0.84[ASN][1000 genomes]
rs6752406	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs744128	0.83[ASN][1000 genomes]
rs749825	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558993	0.84[ASN][1000 genomes]
rs7570764	0.80[ASN][1000 genomes]
rs7571025	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7580128	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586665	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7595524	0.84[ASN][1000 genomes]
rs7598780	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605721	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9283451	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv963883	chr2:134508919-134516201	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6414015	LOC440905	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134508800-134513200	Weak transcription	Fetal Brain Female	brain
2	chr2:134510600-134514200	Enhancers	Fetal Heart	heart
3	chr2:134512400-134514200	Enhancers	Osteobl	bone
4	chr2:134512400-134514600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:134512600-134513400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:134512600-134514200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr2:134512800-134513400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:134512800-134513600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:134512800-134513600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:134512800-134513600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr2:134512800-134513600	Enhancers	Stomach Smooth Muscle	stomach
12	chr2:134512800-134514000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:134512800-134514000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:134512800-134514000	Enhancers	Adipose Nuclei	Adipose
15	chr2:134512800-134514000	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:134512800-134514000	Enhancers	NH-A	brain
17	chr2:134512800-134514200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:134512800-134514200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:134512800-134514200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:134512800-134514200	Enhancers	Colon Smooth Muscle	Colon
21	chr2:134512800-134514200	Enhancers	Fetal Stomach	stomach
22	chr2:134512800-134514200	Enhancers	Lung	lung
23	chr2:134512800-134514200	Enhancers	Ovary	ovary
24	chr2:134512800-134514200	Enhancers	Right Atrium	heart
25	chr2:134512800-134514200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:134512800-134514200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:134512800-134514200	Enhancers	NHDF-Ad	bronchial
28	chr2:134512800-134514400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:134512800-134514400	Enhancers	Fetal Lung	lung
30	chr2:134512800-134514400	Enhancers	Fetal Muscle Leg	muscle
31	chr2:134512800-134514800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:134512800-134514800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:134513000-134513400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr2:134513000-134513400	Weak transcription	Left Ventricle	heart
35	chr2:134513000-134513400	Weak transcription	Right Ventricle	heart
36	chr2:134513000-134513400	Weak transcription	NHLF	lung
37	chr2:134513000-134513800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:134513000-134514000	Weak transcription	Esophagus	oesophagus

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