Variant report

Variant	rs59582399
Chromosome Location	chr9:96286163-96286164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96264104..96265663-chr9:96285613..96287201,2	K562	blood:
2	chr9:96283749..96287240-chr9:96288399..96291092,3	K562	blood:
3	chr9:96211644..96215224-chr9:96285600..96289647,5	MCF-7	breast:
4	chr9:96279743..96281562-chr9:96285341..96286993,2	MCF-7	breast:
5	chr9:96213039..96215979-chr9:96285454..96287500,4	MCF-7	breast:
6	chr9:96283725..96286210-chr9:96295054..96296759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10429558	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11975	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12341488	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12554020	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815563	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4552973	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59483310	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60076242	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6479482	0.83[AMR][1000 genomes]
rs6479483	0.83[AMR][1000 genomes]
rs6479487	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479494	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6479495	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7020459	0.83[AMR][1000 genomes]
rs7023933	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7025805	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7028729	0.83[AMR][1000 genomes]
rs7035657	0.83[AMR][1000 genomes]
rs7036984	0.83[AMR][1000 genomes]
rs7048853	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7850322	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7853605	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7857183	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7860098	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7862998	0.83[AMR][1000 genomes]
rs7870210	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs59582399	HMGB3	trans	lymphoblastoid	RTeQTL
rs59582399	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs59582399	RP11-165J3.6	cis	Stomach	GTEx
rs59582399	RP11-165J3.6	cis	Artery Tibial	GTEx
rs59582399	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs59582399	RP11-165J3.6	cis	Thyroid	GTEx
rs59582399	RP11-165J3.6	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96229600-96286200	Weak transcription	Fetal Brain Male	brain
2	chr9:96243000-96288000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:96260800-96290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96262200-96289000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:96263200-96287600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:96263200-96290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:96263400-96289000	Weak transcription	Fetal Kidney	kidney
8	chr9:96264000-96286600	Weak transcription	NH-A	brain
9	chr9:96264200-96288400	Weak transcription	HSMMtube	muscle
10	chr9:96265800-96286200	Weak transcription	HUVEC	blood vessel
11	chr9:96265800-96286400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:96268000-96286400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr9:96270800-96291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:96273800-96286600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:96274000-96291000	Weak transcription	Small Intestine	intestine
16	chr9:96275800-96299600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:96276000-96295600	Weak transcription	Stomach Mucosa	stomach
18	chr9:96276000-96300000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:96276200-96287800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:96276200-96290200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:96276200-96291400	Weak transcription	Brain Germinal Matrix	brain
22	chr9:96278400-96310800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr9:96278400-96327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:96278400-96327200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr9:96278400-96328200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr9:96278600-96311200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr9:96278800-96286800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:96278800-96298600	Strong transcription	Placenta	Placenta
29	chr9:96279000-96297400	Strong transcription	HepG2	liver
30	chr9:96279000-96298600	Strong transcription	GM12878-XiMat	blood
31	chr9:96279000-96310400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr9:96279000-96327400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:96280000-96288200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:96281200-96286800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:96281200-96287600	Weak transcription	Brain Substantia Nigra	brain
36	chr9:96281400-96295600	Weak transcription	Psoas Muscle	Psoas
37	chr9:96282200-96323400	Strong transcription	Primary B cells from cord blood	blood
38	chr9:96282800-96287600	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:96283000-96297200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:96283200-96287800	Weak transcription	Aorta	Aorta
41	chr9:96283200-96288200	Weak transcription	NHLF	lung
42	chr9:96283200-96289400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:96283200-96291200	Weak transcription	Fetal Brain Female	brain
44	chr9:96283600-96286800	Weak transcription	NHDF-Ad	bronchial
45	chr9:96283600-96297400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:96283800-96287600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr9:96284200-96290600	Enhancers	Fetal Heart	heart
48	chr9:96284400-96297800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:96284600-96327200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:96284600-96328200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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