Variant report

Variant	rs12554164
Chromosome Location	chr9:96218959-96218960
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr9:96218790-96219189	K562	blood:	n/a	n/a
2	TEAD4	chr9:96218627-96219182	K562	blood:	n/a	n/a
3	SPI1	chr9:96218768-96219062	HL-60	blood:	n/a	n/a
4	WRNIP1	chr9:96218844-96219015	GM12878	blood:	n/a	n/a
5	BCL11A	chr9:96218836-96219078	GM12878	blood:	n/a	chr9:96218973-96218982
6	TBL1XR1	chr9:96218928-96219128	K562	blood:	n/a	n/a
7	SPI1	chr9:96218702-96219242	HL-60	blood:	n/a	n/a
8	E2F4	chr9:96218658-96219136	MCF10A-Er-Src	breast:	n/a	n/a
9	EBF1	chr9:96218818-96219225	GM12878	blood:	n/a	n/a
10	RCOR1	chr9:96218934-96219096	K562	blood:	n/a	n/a
11	SPI1	chr9:96218885-96219057	K562	blood:	n/a	n/a
12	SPI1	chr9:96218826-96219132	GM12878	blood:	n/a	n/a
13	ELF1	chr9:96218847-96219141	K562	blood:	n/a	chr9:96218969-96218982
14	EP300	chr9:96218948-96219191	K562	blood:	n/a	n/a
15	MAZ	chr9:96218942-96219183	K562	blood:	n/a	n/a
16	NR2F2	chr9:96218717-96219233	K562	blood:	n/a	n/a
17	MAFF	chr9:96218955-96219325	K562	blood:	n/a	n/a
18	JUND	chr9:96218833-96219099	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95963731..95965841-chr9:96218662..96220646,2	MCF-7	breast:
2	chr9:96217110..96219657-chr9:96251962..96254616,2	K562	blood:

Variant related genes	Relation type
FAM120AOS	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12551084	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12553389	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16909150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909273	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17532098	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1999386	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35383254	1.00[AFR][1000 genomes]
rs35540150	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3893381	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4255201	1.00[CEU][hapmap]
rs55654600	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56025666	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56073019	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56275034	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7035657	0.80[CEU][hapmap]
rs7036984	0.80[CEU][hapmap]
rs7038310	0.82[CEU][hapmap]
rs883783	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs883785	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12554164	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs12554164	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs12554164	RP11-165J3.6	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96216200-96220400	Weak transcription	Pancreas	Pancrea
2	chr9:96216200-96220400	Weak transcription	Spleen	Spleen
3	chr9:96216200-96220600	Weak transcription	Gastric	stomach
4	chr9:96216200-96228800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:96216400-96220600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:96216400-96220600	Weak transcription	Esophagus	oesophagus
7	chr9:96216400-96221000	Weak transcription	Aorta	Aorta
8	chr9:96216400-96230600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:96216600-96219600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr9:96216600-96223400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr9:96216600-96224000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:96216600-96231200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:96216600-96232800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr9:96216800-96219200	Enhancers	Liver	Liver
15	chr9:96216800-96219400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:96216800-96219800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:96216800-96220200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:96216800-96220400	Enhancers	Fetal Intestine Small	intestine
19	chr9:96216800-96220400	Weak transcription	Left Ventricle	heart
20	chr9:96216800-96220400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr9:96216800-96220600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:96216800-96220600	Weak transcription	Placenta	Placenta
23	chr9:96216800-96220600	Weak transcription	Ovary	ovary
24	chr9:96216800-96220600	Weak transcription	Right Ventricle	heart
25	chr9:96216800-96220800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr9:96216800-96222200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:96216800-96222400	Enhancers	HepG2	liver
28	chr9:96216800-96225000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr9:96216800-96230600	Weak transcription	Fetal Stomach	stomach
30	chr9:96216800-96231400	Enhancers	Primary T cells from cord blood	blood
31	chr9:96217000-96219600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:96217000-96219600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr9:96217000-96220000	Weak transcription	Fetal Thymus	thymus
34	chr9:96217000-96220400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:96217000-96220400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr9:96217000-96220400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:96217000-96220600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:96217000-96220600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:96217000-96220600	Weak transcription	Fetal Kidney	kidney
40	chr9:96217000-96220600	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:96217000-96221000	Weak transcription	Brain Anterior Caudate	brain
42	chr9:96217000-96221200	Weak transcription	Brain Substantia Nigra	brain
43	chr9:96217000-96222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:96217000-96226200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:96217200-96219000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr9:96217200-96219200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr9:96217200-96219400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr9:96217200-96219400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr9:96217200-96219800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr9:96217200-96220600	Weak transcription	Brain Inferior Temporal Lobe	brain

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