Variant report

Variant	rs10873777
Chromosome Location	chr1:86860252-86860253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86858845..86860398-chr1:86869035..86871244,2	K562	blood:
2	chr1:86854491..86856100-chr1:86858979..86861323,2	K562	blood:

Variant related genes	Relation type
ENSG00000231349	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493789	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[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];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873782	0.86[CEU][hapmap]
rs1158505	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1334143	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1334145	0.91[CEU][hapmap]
rs1334146	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];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];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166626	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs166627	0.90[AFR][1000 genomes];0.91[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];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185655	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs187971	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1931363	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2104963	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2151708	0.88[AFR][1000 genomes];0.95[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];0.80[ASN][1000 genomes]
rs272491	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272494	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272504	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]
rs272507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272510	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272511	0.96[AFR][1000 genomes];0.95[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];0.95[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];0.85[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];1.00[ASN][1000 genomes]
rs61804060	0.81[ASN][1000 genomes]
rs6695671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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:4 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10873777	SEP15	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
2	chr1:86843400-86860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:86843600-86860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:86843600-86860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:86844800-86861000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:86845000-86860600	Weak transcription	Fetal Thymus	thymus
7	chr1:86845000-86860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:86846600-86860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:86848800-86861000	Weak transcription	Primary B cells from cord blood	blood
10	chr1:86849200-86860800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:86852400-86860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:86855600-86860800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:86855600-86860800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:86855800-86860800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:86855800-86861000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:86856200-86860600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:86857200-86861000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:86858400-86860800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:86858600-86860800	Enhancers	Primary T cells from cord blood	blood
20	chr1:86858600-86860800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:86858600-86860800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:86858800-86860800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:86858800-86860800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:86858800-86860800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:86858800-86860800	Enhancers	Adipose Nuclei	Adipose
26	chr1:86858800-86861000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:86859000-86861200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:86859200-86860800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:86859200-86860800	Enhancers	Brain Germinal Matrix	brain
30	chr1:86859200-86860800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:86859200-86861000	Enhancers	Fetal Stomach	stomach
32	chr1:86859400-86860800	Weak transcription	Brain Anterior Caudate	brain
33	chr1:86859400-86861400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:86859600-86860600	Enhancers	Thymus	Thymus
35	chr1:86859600-86860800	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:86859600-86860800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:86859600-86860800	Enhancers	Fetal Brain Female	brain
38	chr1:86859600-86860800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:86859600-86860800	Active TSS	Hela-S3	cervix
40	chr1:86859600-86861000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:86859600-86861000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:86859600-86862800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:86859800-86860600	Enhancers	HSMM	muscle
44	chr1:86859800-86860800	Weak transcription	Brain Angular Gyrus	brain
45	chr1:86859800-86860800	Weak transcription	Fetal Heart	heart
46	chr1:86859800-86860800	Weak transcription	Fetal Kidney	kidney
47	chr1:86859800-86860800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:86859800-86861000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:86859800-86862200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:86859800-86862400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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