Variant report

Variant	rs12569042
Chromosome Location	chr1:247366380-247366381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10924964	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115202	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12567626	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17269923	1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2380117	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2892054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35229190	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738443	0.80[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41315860	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4269806	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4351686	0.89[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4551629	0.84[CEU][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4582838	0.83[CEU][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55643126	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55914345	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56029850	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56046175	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56065612	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56340510	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58405512	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60240280	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60698393	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61839991	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61839994	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61839996	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61839997	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61840000	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61840048	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61840053	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840054	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61840055	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61840056	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61840057	0.90[EUR][1000 genomes]
rs61840059	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6656425	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6660351	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665647	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666543	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6668154	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680197	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6684181	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6689651	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs6698690	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74152976	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74152988	0.91[AFR][1000 genomes]
rs74152993	0.91[AFR][1000 genomes]
rs7536883	0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546908	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551871	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
9	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
11	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a
12	nsv873437	chr1:247340784-247366380	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	n/a
13	nsv873438	chr1:247347971-247366380	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12569042	RP11-488L18.10	cis	lung	GTEx
rs12569042	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx
rs12569042	OR2M7	cis	parietal	SCAN
rs12569042	RP11-488L18.10	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247346000-247370200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:247346000-247371800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr1:247352000-247368200	ZNF genes & repeats	Liver	Liver
5	chr1:247353000-247367200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:247353000-247368000	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr1:247353000-247370400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:247353400-247372000	ZNF genes & repeats	GM12878-XiMat	blood
9	chr1:247354000-247371000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:247354800-247371200	Weak transcription	Stomach Mucosa	stomach
11	chr1:247354800-247372400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247354800-247372400	Weak transcription	Right Ventricle	heart
13	chr1:247356000-247367200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:247356000-247367800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:247356000-247372400	Weak transcription	Brain Anterior Caudate	brain
16	chr1:247356000-247372400	Weak transcription	Fetal Brain Male	brain
17	chr1:247356000-247372600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:247356000-247372600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:247356200-247372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:247356200-247372400	Weak transcription	Colonic Mucosa	Colon
21	chr1:247356400-247372400	Weak transcription	Gastric	stomach
22	chr1:247356600-247367800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:247357000-247367400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:247357200-247367000	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:247357200-247370800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr1:247357600-247367800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:247357800-247366400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:247358000-247368000	Strong transcription	Fetal Thymus	thymus
29	chr1:247358400-247372400	Weak transcription	Fetal Heart	heart
30	chr1:247359000-247372600	Weak transcription	Fetal Kidney	kidney
31	chr1:247359200-247367000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:247359600-247367600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:247360600-247367200	Strong transcription	K562	blood
34	chr1:247360600-247369000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:247360600-247370400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:247360600-247372400	Weak transcription	Fetal Lung	lung
37	chr1:247360600-247372400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:247361000-247367800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:247361200-247369200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:247361400-247371400	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:247362000-247369400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:247362400-247373400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:247362600-247366600	Weak transcription	Hela-S3	cervix
44	chr1:247362600-247371000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:247362600-247371200	Weak transcription	HepG2	liver
46	chr1:247362600-247372400	Weak transcription	Psoas Muscle	Psoas
47	chr1:247362600-247372800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:247362800-247366800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:247362800-247366800	Weak transcription	NHLF	lung
50	chr1:247362800-247367600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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