Variant report

Variant	rs12554020
Chromosome Location	chr9:96270237-96270238
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96212662..96217709-chr9:96266725..96273295,11	MCF-7	breast:
2	chr9:96268450..96271013-chr9:96286354..96288528,2	K562	blood:
3	chr9:96264790..96266601-chr9:96268569..96271456,2	K562	blood:

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10429558	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10821155	0.81[YRI][hapmap]
rs11975	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12335532	0.81[CEU][hapmap]
rs12341488	0.81[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13292712	0.83[YRI][hapmap]
rs16909211	0.80[YRI][hapmap]
rs3815563	0.91[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3933797	0.81[CEU][hapmap]
rs4552973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59483310	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59582399	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60076242	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6479487	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479493	0.82[YRI][hapmap]
rs6479494	0.81[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6479495	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7019001	0.82[YRI][hapmap]
rs7023933	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7025805	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7035657	0.83[JPT][hapmap]
rs7036984	0.83[JPT][hapmap]
rs7048853	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7850322	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7853605	0.91[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7857183	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7860098	0.82[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7870210	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs952288	0.82[YRI][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12554020	RP11-165J3.6	cis	Stomach	GTEx
rs12554020	HMGB3	trans	lymphoblastoid	RTeQTL
rs12554020	RP11-165J3.6	cis	Nerve Tibial	GTEx
rs12554020	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs12554020	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs12554020	RP11-165J3.6	cis	Thyroid	GTEx
rs12554020	RP11-165J3.6	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 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	chr9:96243400-96271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:96260400-96275600	Weak transcription	Esophagus	oesophagus
5	chr9:96260800-96290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:96262200-96289000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:96263200-96270600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:96263200-96285800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:96263200-96287600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:96263200-96290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:96263400-96289000	Weak transcription	Fetal Kidney	kidney
12	chr9:96263600-96275400	Weak transcription	Brain Germinal Matrix	brain
13	chr9:96263600-96280200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:96264000-96270400	Weak transcription	Pancreas	Pancrea
15	chr9:96264000-96270400	Weak transcription	Thymus	Thymus
16	chr9:96264000-96273000	Weak transcription	Ovary	ovary
17	chr9:96264000-96273200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:96264000-96273400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:96264000-96273400	Weak transcription	Fetal Heart	heart
20	chr9:96264000-96273600	Weak transcription	Brain Angular Gyrus	brain
21	chr9:96264000-96275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:96264000-96280400	Weak transcription	Colonic Mucosa	Colon
23	chr9:96264000-96281600	Weak transcription	Aorta	Aorta
24	chr9:96264000-96286600	Weak transcription	NH-A	brain
25	chr9:96264200-96275400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr9:96264200-96281800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:96264200-96288400	Weak transcription	HSMMtube	muscle
28	chr9:96264600-96271600	Strong transcription	Primary T cells from cord blood	blood
29	chr9:96265400-96275400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:96265800-96270400	Weak transcription	HMEC	breast
31	chr9:96265800-96273600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:96265800-96275600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:96265800-96278400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:96265800-96286200	Weak transcription	HUVEC	blood vessel
35	chr9:96265800-96286400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:96266000-96272200	Weak transcription	A549	lung
37	chr9:96266000-96273400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:96266000-96273600	Weak transcription	Brain Anterior Caudate	brain
39	chr9:96266000-96274000	Weak transcription	NHLF	lung
40	chr9:96266000-96275600	Weak transcription	Fetal Brain Female	brain
41	chr9:96266000-96279800	Weak transcription	HSMM	muscle
42	chr9:96266400-96271200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:96266600-96270400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:96266600-96275600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:96266600-96279200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:96266800-96270400	Weak transcription	HepG2	liver
47	chr9:96266800-96274200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:96267200-96270400	Weak transcription	Placenta	Placenta
49	chr9:96267200-96271000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:96267200-96271000	Weak transcription	Fetal Intestine Large	intestine

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