Variant report

Variant	rs36125117
Chromosome Location	chr1:62398246-62398247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10889273	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11585194	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11801995	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11804927	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11810455	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12724144	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12725114	0.91[EUR][1000 genomes]
rs12725290	0.91[EUR][1000 genomes]
rs12731725	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12735117	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12740631	0.90[EUR][1000 genomes]
rs12748525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12753435	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17122871	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17122873	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17313118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17378746	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2185136	1.00[YRI][hapmap]
rs2365734	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2365738	0.83[TSI][hapmap]
rs2482893	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2482894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2498967	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs2498973	0.85[CEU][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2498975	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2886446	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2886448	0.83[TSI][hapmap]
rs34158435	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34189113	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34843158	0.90[EUR][1000 genomes]
rs34896171	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35814605	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35899620	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66606678	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6667051	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6685239	0.82[TSI][hapmap]
rs67395722	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67412592	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67786436	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7514549	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7526836	0.83[TSI][hapmap]
rs7529379	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7553347	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1110	chr1:62395723-62454435	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs36125117	OMA1	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62336000-62408600	Weak transcription	Pancreas	Pancrea
2	chr1:62340400-62399200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:62346200-62417600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:62350600-62428200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:62350800-62417600	Weak transcription	Ovary	ovary
6	chr1:62353800-62408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:62361600-62408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:62362000-62408600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:62372400-62408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:62372400-62417600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:62374600-62410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:62375200-62404600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:62376200-62417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:62380600-62408600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:62380800-62410000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:62381000-62408200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:62381000-62416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:62381200-62417400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:62381200-62418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:62381600-62402800	Weak transcription	HepG2	liver
21	chr1:62383400-62408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:62384600-62403000	Weak transcription	Fetal Stomach	stomach
23	chr1:62384600-62408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:62384600-62408800	Weak transcription	Fetal Intestine Large	intestine
25	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
26	chr1:62385400-62408400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:62385400-62408600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:62386000-62408600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:62391800-62409000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:62392000-62408800	Weak transcription	Gastric	stomach
31	chr1:62392600-62408600	Weak transcription	Stomach Mucosa	stomach
32	chr1:62392600-62408800	Weak transcription	Left Ventricle	heart
33	chr1:62393800-62402800	Weak transcription	Hela-S3	cervix
34	chr1:62393800-62422400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:62394800-62400400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:62395000-62408600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:62395000-62410800	Weak transcription	Liver	Liver
38	chr1:62395400-62398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:62395800-62408200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:62396200-62408600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:62396200-62416000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:62396200-62417200	Weak transcription	HMEC	breast
43	chr1:62396400-62408200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:62396400-62408600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:62396400-62418000	Weak transcription	Fetal Kidney	kidney
46	chr1:62397000-62398600	Strong transcription	Fetal Intestine Small	intestine
47	chr1:62397000-62400400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:62397200-62398400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:62397400-62398800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:62397400-62408200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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