Variant report

Variant	rs12553389
Chromosome Location	chr9:96263261-96263262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96244925..96246887-chr9:96262831..96264712,2	K562	blood:
2	chr9:96212252..96216666-chr9:96261096..96265019,5	K562	blood:
3	chr9:96252755..96257145-chr9:96262506..96266410,6	MCF-7	breast:
4	chr9:96213983..96216666-chr9:96261096..96263660,2	K562	blood:
5	chr9:96259081..96260977-chr9:96262219..96263886,2	K562	blood:
6	chr9:96261936..96263563-chr9:96264731..96266679,2	MCF-7	breast:
7	chr9:96214092..96216471-chr9:96262447..96264287,3	MCF-7	breast:
8	chr9:96263050..96265153-chr9:96327344..96330219,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263875	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12551084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554164	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	0.88[CEU][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]
rs16909158	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]
rs16909273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532098	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1999386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383254	1.00[AFR][1000 genomes]
rs35540150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255201	0.88[CEU][hapmap]
rs55654600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025666	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56073019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56275034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038310	0.82[CEU][hapmap]
rs883783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12553389	RP11-165J3.6	cis	Thyroid	GTEx
rs12553389	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs12553389	RP11-165J3.6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 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	chr9:96250400-96266000	Strong transcription	Fetal Muscle Trunk	muscle
5	chr9:96254800-96266600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:96255200-96266800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:96255200-96267200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:96255400-96268400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:96255800-96266200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:96255800-96266800	Strong transcription	HepG2	liver
11	chr9:96256000-96265000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:96256400-96265400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:96256400-96265800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:96256400-96267200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:96256600-96265800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:96256800-96269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:96257200-96264000	Strong transcription	Fetal Intestine Small	intestine
18	chr9:96257200-96267200	Strong transcription	Fetal Intestine Large	intestine
19	chr9:96258200-96263600	Strong transcription	Brain Germinal Matrix	brain
20	chr9:96258800-96267200	Strong transcription	Fetal Lung	lung
21	chr9:96259000-96263400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr9:96259600-96263400	Strong transcription	Fetal Kidney	kidney
23	chr9:96260400-96275600	Weak transcription	Esophagus	oesophagus
24	chr9:96260800-96290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:96261000-96264000	Enhancers	Fetal Heart	heart
26	chr9:96261800-96263400	Strong transcription	HSMM	muscle
27	chr9:96262000-96263400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:96262200-96263400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:96262200-96263400	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr9:96262200-96263400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr9:96262200-96263400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr9:96262200-96263600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:96262200-96263800	Enhancers	Psoas Muscle	Psoas
34	chr9:96262200-96264000	Genic enhancers	Left Ventricle	heart
35	chr9:96262200-96264000	Enhancers	Stomach Mucosa	stomach
36	chr9:96262200-96289000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:96262400-96263400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:96262400-96263400	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr9:96262400-96263400	Enhancers	Osteobl	bone
40	chr9:96262400-96263600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:96262400-96263600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr9:96262400-96263600	Genic enhancers	Fetal Thymus	thymus
43	chr9:96262400-96264000	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr9:96262400-96264200	Genic enhancers	Fetal Stomach	stomach
45	chr9:96262600-96263400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr9:96262600-96263600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:96262600-96263600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr9:96262600-96264000	Genic enhancers	Placenta	Placenta
49	chr9:96262600-96264000	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr9:96262600-96264200	Genic enhancers	Primary B cells from peripheral blood	blood

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