Variant report

Variant	rs16909158
Chromosome Location	chr9:96220164-96220165
allele	A/G
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	GATA3	chr9:96219795-96220334	MCF-7	breast:	n/a	chr9:96220132-96220142
2	GATA3	chr9:96219985-96220219	MCF-7	breast:	n/a	chr9:96220132-96220142

No.	Distal block	Cell Line	Cell type
1	chr9:96220139..96221974-chr9:96287391..96289442,3	MCF-7	breast:
2	chr9:95963731..95965841-chr9:96218662..96220646,2	MCF-7	breast:
3	chr9:96219136..96220997-chr9:96281166..96283983,2	MCF-7	breast:

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]
rs12554164	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]
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]
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
rs16909158	RP11-165J3.6	cis	Thyroid	GTEx
rs16909158	RP11-165J3.6	cis	Esophagus Muscularis	GTEx
rs16909158	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 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	chr9:96216600-96223400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr9:96216600-96224000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:96216600-96231200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:96216600-96232800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr9:96216800-96220200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr9:96216800-96220400	Enhancers	Fetal Intestine Small	intestine
15	chr9:96216800-96220400	Weak transcription	Left Ventricle	heart
16	chr9:96216800-96220400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr9:96216800-96220600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:96216800-96220600	Weak transcription	Placenta	Placenta
19	chr9:96216800-96220600	Weak transcription	Ovary	ovary
20	chr9:96216800-96220600	Weak transcription	Right Ventricle	heart
21	chr9:96216800-96220800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr9:96216800-96222200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:96216800-96222400	Enhancers	HepG2	liver
24	chr9:96216800-96225000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr9:96216800-96230600	Weak transcription	Fetal Stomach	stomach
26	chr9:96216800-96231400	Enhancers	Primary T cells from cord blood	blood
27	chr9:96217000-96220400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:96217000-96220400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr9:96217000-96220400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:96217000-96220600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:96217000-96220600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:96217000-96220600	Weak transcription	Fetal Kidney	kidney
33	chr9:96217000-96220600	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:96217000-96221000	Weak transcription	Brain Anterior Caudate	brain
35	chr9:96217000-96221200	Weak transcription	Brain Substantia Nigra	brain
36	chr9:96217000-96222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:96217000-96226200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:96217200-96220600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:96217200-96221200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr9:96217200-96221400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:96217200-96239800	Weak transcription	Fetal Brain Female	brain
42	chr9:96217400-96220200	Weak transcription	Colonic Mucosa	Colon
43	chr9:96217400-96220400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:96217400-96220600	Weak transcription	Right Atrium	heart
45	chr9:96217400-96220800	Weak transcription	Fetal Lung	lung
46	chr9:96217400-96221400	Weak transcription	HSMMtube	muscle
47	chr9:96217400-96222800	Weak transcription	Thymus	Thymus
48	chr9:96217400-96223200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:96217400-96228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:96217400-96230800	Weak transcription	HSMM	muscle

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