Variant report

Variant	rs9806410
Chromosome Location	chr15:40851755-40851756
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40849898..40854344-chr15:40855565..40858408,6	K562	blood:
2	chr15:40729710..40731654-chr15:40849849..40851885,2	MCF-7	breast:
3	chr15:40851612..40853360-chr15:40855427..40858300,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128891	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1051482	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs10851396	0.95[CEU][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11070279	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070285	0.80[CEU][hapmap]
rs11070286	0.80[CEU][hapmap]
rs11852479	0.87[EUR][1000 genomes]
rs11852694	0.80[CEU][hapmap]
rs11855334	0.80[CEU][hapmap]
rs11855923	0.80[CEU][hapmap]
rs11857247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11858113	0.80[CEU][hapmap]
rs12148185	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs12899408	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12905162	0.80[CEU][hapmap]
rs12906755	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs12907448	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs12907984	0.88[EUR][1000 genomes]
rs12908114	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12908443	0.84[EUR][1000 genomes]
rs12908867	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12914501	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915563	0.91[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12916323	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs1453183	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16970851	0.80[CEU][hapmap]
rs17746659	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17747399	0.88[EUR][1000 genomes]
rs2123534	0.82[EUR][1000 genomes]
rs2304583	0.91[CEU][hapmap]
rs2412531	0.80[CEU][hapmap]
rs2412544	0.80[CEU][hapmap]
rs2412545	0.91[CEU][hapmap]
rs3213999	0.86[CEU][hapmap]
rs34303240	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34750756	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35047458	0.80[CEU][hapmap]
rs35884042	0.88[EUR][1000 genomes]
rs3743146	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3751653	0.80[CEU][hapmap]
rs3803353	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4457966	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs4923876	0.80[CEU][hapmap]
rs4924481	0.80[CEU][hapmap]
rs5030783	0.91[CEU][hapmap]
rs55954396	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56384845	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61048252	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62018048	0.82[EUR][1000 genomes]
rs62018051	0.85[EUR][1000 genomes]
rs62019866	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62019883	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6582	0.80[CEU][hapmap]
rs7162749	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164385	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165054	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7181909	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72733469	0.85[EUR][1000 genomes]
rs731640	0.82[CEU][hapmap]
rs733299	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs8025458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026605	0.80[CEU][hapmap]
rs8028910	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs8029384	0.80[CEU][hapmap]
rs8036938	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038396	0.83[EUR][1000 genomes]
rs8041534	0.80[CEU][hapmap]
rs8042733	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs999197	0.96[CEU][hapmap]

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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs9806410	CCDC32	cis	multi-tissue	Pritchard
rs9806410	C15orf57	cis	Stomach	GTEx
rs9806410	CCDC32	cis	normal skin	skin_eQTL
rs9806410	RP11-111A22.1	cis	lung	GTEx
rs9806410	C15orf57	cis	lung	GTEx
rs9806410	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs9806410	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs9806410	C15orf57	cis	Adipose Subcutaneous	GTEx
rs9806410	CCDC32	cis	lesional skin	skin_eQTL
rs9806410	C15orf57	cis	Nerve Tibial	GTEx
rs9806410	C15orf57	cis	Artery Aorta	GTEx
rs9806410	C15orf57	cis	Muscle Skeletal	GTEx
rs9806410	ZFYVE19	cis	multi-tissue	Pritchard
rs9806410	C15orf57	cis	Artery Tibial	GTEx
rs9806410	C15orf57	cis	Lymphoblastoid	GTEx
rs9806410	C15orf57	cis	Esophagus Muscularis	GTEx
rs9806410	C15orf57	cis	Cerebellum	GTEx
rs9806410	C15orf57	cis	Esophagus Mucosa	GTEx
rs9806410	RP11-111A22.1	cis	Stomach	GTEx
rs9806410	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs9806410	MGC20481	cis	multi-tissue	Pritchard
rs9806410	RP11-111A22.1	cis	Artery Tibial	GTEx
rs9806410	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs9806410	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs9806410	RP11-111A22.1	cis	Artery Aorta	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
3	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40838000-40856400	Weak transcription	A549	lung
6	chr15:40838600-40852800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
9	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
11	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
12	chr15:40843800-40856400	Weak transcription	HSMMtube	muscle
13	chr15:40846000-40855600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:40846200-40855000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:40846200-40856200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:40846400-40853400	Weak transcription	Thymus	Thymus
17	chr15:40846600-40853800	Weak transcription	Spleen	Spleen
18	chr15:40846600-40855000	Weak transcription	Psoas Muscle	Psoas
19	chr15:40846600-40855800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:40846600-40856400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:40846600-40856400	Weak transcription	Right Atrium	heart
22	chr15:40846600-40856600	Weak transcription	Aorta	Aorta
23	chr15:40846600-40856600	Weak transcription	Gastric	stomach
24	chr15:40846800-40856000	Weak transcription	Stomach Mucosa	stomach
25	chr15:40847200-40855000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:40847200-40855600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:40847200-40856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:40847400-40855000	Weak transcription	Fetal Brain Male	brain
29	chr15:40847400-40856200	Weak transcription	Brain Germinal Matrix	brain
30	chr15:40847400-40856400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:40847400-40856600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:40848000-40854000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:40848000-40856400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:40848000-40856400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:40848000-40856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:40848000-40856400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:40848400-40854400	Weak transcription	Hela-S3	cervix
38	chr15:40848400-40856400	Weak transcription	NHDF-Ad	bronchial
39	chr15:40848600-40852600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:40848600-40853800	Weak transcription	Right Ventricle	heart
41	chr15:40848600-40854000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:40848600-40854000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:40848600-40854200	Weak transcription	Ovary	ovary
44	chr15:40848600-40854200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:40848600-40855000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:40848600-40855000	Weak transcription	Brain Anterior Caudate	brain
47	chr15:40848600-40855200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:40848600-40855800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr15:40848600-40856000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:40848600-40856200	Weak transcription	Brain Cingulate Gyrus	brain

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