Variant report

Variant	rs425437
Chromosome Location	chr1:220868508-220868509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2960571	0.95[AFR][1000 genomes]
rs364360	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs405682	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs415273	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416768	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs437078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439513	0.84[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9431295	0.85[ASW][hapmap];0.85[YRI][hapmap];0.81[AFR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs425437	MOSC1	cis	Lymphoblastoid	GTEx
rs425437	MOSC1	cis	multi-tissue	Pritchard
rs425437	MOSC1	cis	lymphoblastoid	seeQTL
rs425437	C1orf115	cis	multi-tissue	Pritchard
rs425437	MOSC2	cis	multi-tissue	Pritchard
rs425437	MOSC2	cis	lymphoblastoid	seeQTL
rs425437	FLJ14146	cis	multi-tissue	Pritchard
rs425437	C1orf115	cis	Lymphoblastoid	GTEx
rs425437	C1orf115	cis	lymphoblastoid	seeQTL
rs425437	MOSC2	cis	Lymphoblastoid	GTEx
rs425437	FLJ20605	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220864200-220870000	Weak transcription	Aorta	Aorta
2	chr1:220864400-220869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:220865000-220870200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:220865000-220870200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:220865200-220870200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:220865200-220873200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:220865200-220874200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:220865200-220879200	Weak transcription	Ovary	ovary
9	chr1:220865400-220870000	Weak transcription	Left Ventricle	heart
10	chr1:220865400-220870000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:220865400-220870200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:220865400-220870200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:220865400-220870200	Weak transcription	Right Ventricle	heart
14	chr1:220865400-220870800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:220865400-220873200	Weak transcription	Fetal Brain Female	brain
16	chr1:220865400-220873800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:220865400-220874400	Weak transcription	Colonic Mucosa	Colon
18	chr1:220865400-220876200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:220865600-220870200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:220865600-220870800	Weak transcription	Brain Anterior Caudate	brain
21	chr1:220866000-220872400	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:220866000-220873400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:220866000-220873600	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:220866200-220868600	Enhancers	HepG2	liver
25	chr1:220866200-220869800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:220866400-220868600	Enhancers	Fetal Intestine Large	intestine
27	chr1:220866600-220872400	Weak transcription	Fetal Brain Male	brain
28	chr1:220866600-220879600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:220867200-220869800	Enhancers	Placenta	Placenta
30	chr1:220867200-220870000	Weak transcription	Adipose Nuclei	Adipose
31	chr1:220867200-220870600	Weak transcription	Fetal Lung	lung
32	chr1:220867800-220869000	Weak transcription	Liver	Liver
33	chr1:220867800-220870400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr1:220868400-220868600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:220868400-220868800	Enhancers	Gastric	stomach
36	chr1:220868400-220868800	Enhancers	Lung	lung
37	chr1:220868400-220868800	Enhancers	Pancreas	Pancrea
38	chr1:220868400-220868800	Enhancers	Spleen	Spleen
39	chr1:220868400-220873200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:220868400-220873600	Strong transcription	Fetal Intestine Small	intestine

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