Variant report

Variant	rs2667970
Chromosome Location	chr1:220432881-220432882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10863537	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10863538	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11118507	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026681	0.95[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs1397958	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588578	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221833	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667967	0.92[EUR][1000 genomes]
rs2667968	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667969	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808008	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808009	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808011	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808012	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808013	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808016	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808018	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808019	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814492	0.96[ASN][1000 genomes]
rs2814494	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2814495	0.94[ASN][1000 genomes]
rs4142940	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4511114	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6541127	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696985	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535619	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4643	chr1:220397642-220442231	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv945297	chr1:220426814-220434679	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2667970	MOSC2	cis	lymphoblastoid	seeQTL
rs2667970	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220393000-220441000	Weak transcription	NHDF-Ad	bronchial
2	chr1:220416000-220442600	Weak transcription	Fetal Heart	heart
3	chr1:220421000-220436800	Weak transcription	Fetal Kidney	kidney
4	chr1:220423000-220443400	Weak transcription	Psoas Muscle	Psoas
5	chr1:220423400-220443400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:220423400-220443400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:220423600-220440400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:220423800-220442600	Weak transcription	Hela-S3	cervix
9	chr1:220424400-220439600	Weak transcription	HMEC	breast
10	chr1:220425200-220443400	Weak transcription	HUVEC	blood vessel
11	chr1:220426200-220433200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:220426200-220440200	Weak transcription	Gastric	stomach
13	chr1:220426200-220441800	Weak transcription	Small Intestine	intestine
14	chr1:220426400-220439600	Weak transcription	HSMMtube	muscle
15	chr1:220426600-220435800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:220426600-220436400	Weak transcription	A549	lung
17	chr1:220426600-220436800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:220426600-220439000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:220426600-220439800	Weak transcription	NHEK	skin
20	chr1:220426600-220440000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:220426600-220440200	Weak transcription	NHLF	lung
22	chr1:220426600-220440600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:220426600-220443400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:220426600-220443400	Weak transcription	Right Ventricle	heart
25	chr1:220426600-220444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:220426800-220436600	Weak transcription	Left Ventricle	heart
27	chr1:220426800-220436600	Weak transcription	Osteobl	bone
28	chr1:220426800-220436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:220426800-220437800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:220426800-220438600	Weak transcription	HSMM	muscle
31	chr1:220426800-220438800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:220426800-220438800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:220426800-220439000	Weak transcription	Adipose Nuclei	Adipose
34	chr1:220426800-220439200	Weak transcription	NH-A	brain
35	chr1:220426800-220439400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:220426800-220439600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:220426800-220439800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:220426800-220440000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:220426800-220440000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:220426800-220440000	Weak transcription	Placenta	Placenta
41	chr1:220426800-220441800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:220426800-220441800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:220426800-220442800	Weak transcription	Esophagus	oesophagus
44	chr1:220426800-220443400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:220426800-220443400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:220426800-220443400	Weak transcription	Ovary	ovary
47	chr1:220426800-220444000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:220426800-220444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:220426800-220444400	Weak transcription	Colonic Mucosa	Colon
50	chr1:220426800-220445000	Weak transcription	Aorta	Aorta

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