Variant report

Variant	rs17532098
Chromosome Location	chr9:96262725-96262726
allele	C/T
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	chr9:96248016..96251380-chr9:96259927..96262755,3	MCF-7	breast:
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	chr9:96261356..96262938-chr9:96267899..96270000,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10761208	1.00[CHB][hapmap]
rs12551084	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12552323	0.85[CEU][hapmap]
rs12553389	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12554164	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16909150	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16909158	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16909273	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1999386	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2001609	0.82[CEU][hapmap]
rs35540150	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3829059	0.85[CEU][hapmap]
rs3893381	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4255201	0.85[CEU][hapmap]
rs55654600	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56025666	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56073019	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56275034	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7033532	0.85[CEU][hapmap]
rs7038293	0.82[CEU][hapmap]
rs7038310	1.00[CEU][hapmap]
rs883783	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs883785	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17532098	RP11-165J3.6	cis	Thyroid	GTEx
rs17532098	RP11-165J3.6	cis	Skin Sun Exposed Lower leg	GTEx
rs17532098	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	chr9:96239600-96263200	Weak transcription	Small Intestine	intestine
3	chr9:96243000-96288000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:96243400-96271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:96250400-96266000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr9:96253200-96263000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:96254600-96263000	Strong transcription	Thymus	Thymus
8	chr9:96254600-96263200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:96254800-96263200	Strong transcription	Primary B cells from cord blood	blood
10	chr9:96254800-96263200	Strong transcription	Fetal Muscle Leg	muscle
11	chr9:96254800-96266600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:96255200-96266800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:96255200-96267200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:96255400-96268400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:96255600-96263000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr9:96255800-96263200	Strong transcription	GM12878-XiMat	blood
17	chr9:96255800-96266200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:96255800-96266800	Strong transcription	HepG2	liver
19	chr9:96256000-96263000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:96256000-96263200	Strong transcription	K562	blood
21	chr9:96256000-96265000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:96256400-96263200	Strong transcription	NH-A	brain
23	chr9:96256400-96265400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:96256400-96265800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:96256400-96267200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:96256600-96262800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:96256600-96262800	Strong transcription	HMEC	breast
28	chr9:96256600-96263200	Strong transcription	NHLF	lung
29	chr9:96256600-96265800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:96256800-96263000	Strong transcription	HUVEC	blood vessel
31	chr9:96256800-96269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:96257200-96264000	Strong transcription	Fetal Intestine Small	intestine
33	chr9:96257200-96267200	Strong transcription	Fetal Intestine Large	intestine
34	chr9:96258000-96263000	Weak transcription	Right Ventricle	heart
35	chr9:96258200-96263200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr9:96258200-96263600	Strong transcription	Brain Germinal Matrix	brain
37	chr9:96258400-96263000	Strong transcription	Colonic Mucosa	Colon
38	chr9:96258600-96262800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:96258600-96263200	Strong transcription	Rectal Smooth Muscle	rectum
40	chr9:96258800-96262800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr9:96258800-96267200	Strong transcription	Fetal Lung	lung
42	chr9:96259000-96263400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr9:96259200-96262800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:96259400-96263200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr9:96259600-96263000	Strong transcription	Brain Anterior Caudate	brain
46	chr9:96259600-96263000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:96259600-96263400	Strong transcription	Fetal Kidney	kidney
48	chr9:96259800-96262800	Weak transcription	HSMMtube	muscle
49	chr9:96260000-96263200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:96260200-96263000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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