Variant report

Variant	rs2290941
Chromosome Location	chr15:34544351-34544352
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:34542486..34546422-chr15:34628917..34632698,3	K562	blood:
2	chr15:34542779..34546131-chr15:34549180..34553108,3	K562	blood:
3	chr15:34543302..34545799-chr15:34603176..34605145,2	K562	blood:
4	chr15:34542868..34546239-chr15:34629699..34632698,3	K562	blood:
5	chr15:34539135..34541437-chr15:34542575..34545570,3	K562	blood:
6	chr15:34536358..34538265-chr15:34542430..34544834,2	K562	blood:

Variant related genes	Relation type
ENSG00000140199	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10851964	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1133154	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs12050753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16958835	0.82[CHD][hapmap]
rs16958878	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16958954	0.85[YRI][hapmap]
rs17236763	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236777	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236784	0.86[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17817800	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17817806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244040	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs2290940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705343	0.84[ASW][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4238572	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4530104	0.86[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4577050	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4780231	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4780232	0.84[ASN][1000 genomes]
rs4780233	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4780234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56761496	0.96[ASN][1000 genomes]
rs57494441	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57626952	0.84[ASN][1000 genomes]
rs59023791	0.94[ASN][1000 genomes]
rs59091709	0.93[ASN][1000 genomes]
rs59209438	0.96[ASN][1000 genomes]
rs59712831	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60165224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60604568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61549125	0.96[ASN][1000 genomes]
rs6495639	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6495646	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7168761	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs7178002	0.85[CHD][hapmap]
rs73386033	0.94[ASN][1000 genomes]
rs73386037	0.94[ASN][1000 genomes]
rs73386038	0.94[ASN][1000 genomes]
rs73388003	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73388020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73388027	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73388046	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73388049	0.89[ASN][1000 genomes]
rs8035954	0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs8036468	0.86[CHD][hapmap]
rs8040071	0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1798578	chr15:34543021-34988247	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	esv1804312	chr15:34543021-34988247	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1821622	chr15:34543021-34988247	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	esv1850950	chr15:34543021-34988247	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	esv2758376	chr15:34543021-34988247	Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	esv2760024	chr15:34543021-34988247	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv428303	chr15:34543021-34988247	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2290941	NOP10	cis	Muscle Skeletal	GTEx
rs2290941	NOP10	cis	Heart Left Ventricle	GTEx
rs2290941	NOP10	cis	Esophagus Muscularis	GTEx
rs2290941	NOP10	cis	Esophagus Mucosa	GTEx
rs2290941	NOP10	cis	Thyroid	GTEx
rs2290941	NOP10	cis	parietal	SCAN
rs2290941	TMEM85	cis	cerebellum	SCAN
rs2290941	NOP10	cis	Artery Tibial	GTEx
rs2290941	NOP10	cis	cerebellum	SCAN
rs2290941	SLC12A6	cis	Thyroid	GTEx
rs2290941	NOP10	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
2	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:34519400-34552200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:34519400-34552200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:34519600-34553600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:34519800-34544800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:34520200-34555600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:34521000-34547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:34523000-34545600	Weak transcription	Dnd41	blood
13	chr15:34524200-34552400	Strong transcription	Primary B cells from cord blood	blood
14	chr15:34524800-34553600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:34528400-34546400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:34528400-34547400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:34528600-34554600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:34529000-34554800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:34529200-34546000	Weak transcription	Gastric	stomach
20	chr15:34529200-34550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:34529200-34552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:34529800-34546200	Weak transcription	Esophagus	oesophagus
23	chr15:34531400-34546000	Weak transcription	Spleen	Spleen
24	chr15:34531400-34546400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:34532000-34546000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:34533000-34545800	Weak transcription	Hela-S3	cervix
27	chr15:34533000-34548400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:34533000-34555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:34533000-34556600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:34533000-34564000	Weak transcription	NHLF	lung
31	chr15:34533200-34547200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:34533200-34548200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:34533200-34549400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:34533200-34551200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:34533200-34557400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:34533200-34562800	Weak transcription	Pancreas	Pancrea
37	chr15:34533400-34545200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:34534000-34546400	Weak transcription	Fetal Kidney	kidney
39	chr15:34534400-34546400	Weak transcription	Fetal Heart	heart
40	chr15:34534800-34544800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:34535200-34552200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:34535400-34551200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:34535600-34551200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:34535800-34545000	Weak transcription	HUVEC	blood vessel
45	chr15:34536800-34547600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:34538200-34545800	Weak transcription	Colonic Mucosa	Colon
47	chr15:34538800-34549000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:34539200-34546000	Weak transcription	Fetal Intestine Small	intestine
49	chr15:34539200-34546000	Weak transcription	Fetal Stomach	stomach
50	chr15:34539400-34546000	Weak transcription	NHEK	skin

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