Variant report

Variant	rs426020
Chromosome Location	chr1:220874101-220874102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11118593	0.84[EUR][1000 genomes]
rs1690714	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2069044	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2994525	0.85[EUR][1000 genomes]
rs337153	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs337154	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs337172	0.82[EUR][1000 genomes]
rs365798	0.90[GIH][hapmap]
rs369049	0.94[CEU][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs381106	0.94[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs383681	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3849288	0.89[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs389499	0.84[AMR][1000 genomes]
rs405196	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs414838	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs416735	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs427216	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs438597	0.94[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs442236	0.94[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs7555109	0.87[EUR][1000 genomes]
rs774132	0.89[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs774134	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs774145	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774146	0.87[EUR][1000 genomes]
rs9431295	0.83[TSI][hapmap];0.85[AMR][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	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs426020	MOSC2	cis	lymphoblastoid	seeQTL
rs426020	C1orf115	cis	cerebellum	SCAN
rs426020	C1orf115	cis	lymphoblastoid	seeQTL
rs426020	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs426020	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs426020	EPRS	cis	parietal	SCAN
rs426020	C1orf115	cis	Esophagus Muscularis	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220865200-220874200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:220865200-220879200	Weak transcription	Ovary	ovary
3	chr1:220865400-220874400	Weak transcription	Colonic Mucosa	Colon
4	chr1:220865400-220876200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:220866600-220879600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:220871400-220876200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:220871600-220878400	Weak transcription	Gastric	stomach
8	chr1:220871800-220876600	Weak transcription	Spleen	Spleen
9	chr1:220871800-220878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:220872000-220874400	Enhancers	Placenta	Placenta
11	chr1:220872000-220874600	Enhancers	HepG2	liver
12	chr1:220872000-220875600	Weak transcription	Lung	lung
13	chr1:220872200-220878800	Weak transcription	Fetal Intestine Large	intestine
14	chr1:220872400-220874600	Enhancers	Colon Smooth Muscle	Colon
15	chr1:220872400-220875600	Enhancers	Fetal Brain Male	brain
16	chr1:220872600-220875200	Enhancers	Adipose Nuclei	Adipose
17	chr1:220872800-220876000	Weak transcription	Liver	Liver
18	chr1:220873000-220874800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:220873200-220874400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:220873200-220874400	Enhancers	Brain Angular Gyrus	brain
21	chr1:220873200-220874400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:220873200-220874600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:220873200-220874600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:220873200-220874800	Enhancers	Right Atrium	heart
25	chr1:220873200-220877200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:220873400-220874400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:220873400-220874400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:220873400-220874400	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:220873400-220874400	Enhancers	Fetal Lung	lung
30	chr1:220873400-220874600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:220873400-220876600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:220873400-220878800	Weak transcription	Pancreas	Pancrea
33	chr1:220873600-220874400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:220873600-220874400	Enhancers	Brain Germinal Matrix	brain
35	chr1:220873600-220874400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:220873600-220874400	Enhancers	Fetal Heart	heart
37	chr1:220873600-220874600	Enhancers	Brain Hippocampus Middle	brain
38	chr1:220873600-220878200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:220873600-220879400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:220873800-220874200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:220873800-220874400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr1:220873800-220874600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr1:220873800-220875200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:220873800-220875200	Weak transcription	GM12878-XiMat	blood
45	chr1:220873800-220875200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:220873800-220876000	Weak transcription	Left Ventricle	heart
47	chr1:220873800-220878400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:220873800-220878400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:220873800-220880000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:220874000-220874200	Enhancers	Fetal Brain Female	brain

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