Variant report

Variant	rs272504
Chromosome Location	chr1:86833653-86833654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10493789	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747328	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873782	0.86[CEU][hapmap]
rs1158505	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182102	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1334143	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1334145	0.91[CEU][hapmap]
rs1334146	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1334147	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1334148	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166626	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs166627	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17129078	0.81[ASN][1000 genomes]
rs175363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185655	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs187971	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931363	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2104963	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2151708	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2151709	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2250857	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs272491	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272492	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272494	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272510	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272511	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272516	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765975	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs405424	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4288573	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61804060	0.81[ASN][1000 genomes]
rs6695671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883200	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1793594	chr1:86833653-86858957	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs272504	ODF2L	cis	multi-tissue	Pritchard
rs272504	SEP15	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:86813800-86836400	Weak transcription	Lung	lung
3	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
4	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
5	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
7	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:86817800-86835400	Weak transcription	Esophagus	oesophagus
9	chr1:86817800-86840000	Weak transcription	GM12878-XiMat	blood
10	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
12	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
13	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:86818200-86841000	Weak transcription	Fetal Kidney	kidney
15	chr1:86819000-86838400	Weak transcription	NHDF-Ad	bronchial
16	chr1:86819800-86839400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:86819800-86839400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:86819800-86840200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:86819800-86840200	Weak transcription	HMEC	breast
20	chr1:86819800-86842200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:86819800-86842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:86819800-86843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:86819800-86843000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:86820200-86840200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:86820200-86841200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:86820200-86842600	Weak transcription	Brain Germinal Matrix	brain
27	chr1:86820200-86843400	Weak transcription	Left Ventricle	heart
28	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
30	chr1:86820400-86835000	Weak transcription	HSMM	muscle
31	chr1:86820400-86838400	Weak transcription	Primary B cells from cord blood	blood
32	chr1:86820400-86838400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:86820400-86838400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:86820400-86838600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:86820400-86839400	Weak transcription	NH-A	brain
36	chr1:86820400-86842400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:86820400-86842800	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:86820400-86842800	Weak transcription	Placenta	Placenta
39	chr1:86820400-86845400	Weak transcription	Hela-S3	cervix
40	chr1:86820400-86846200	Weak transcription	NHLF	lung
41	chr1:86820400-86846400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:86820400-86847000	Weak transcription	Liver	Liver
43	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:86820400-86860200	Weak transcription	NHEK	skin
45	chr1:86820600-86838400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:86820600-86839400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:86820600-86839400	Weak transcription	Osteobl	bone
48	chr1:86820600-86839600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:86820600-86839600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:86820600-86840000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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