Variant report

Variant	rs9400653
Chromosome Location	chr6:113991145-113991146
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:113986306..113987882-chr6:113989407..113992335,2	MCF-7	breast:
2	chr6:113988623..113991575-chr6:114178978..114181550,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10872102	0.88[ASN][1000 genomes]
rs12176307	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277834	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4142803	0.83[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs4945501	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945964	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4945966	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4945967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945968	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs773692	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9374415	0.83[ASN][1000 genomes]
rs9374416	0.84[ASN][1000 genomes]
rs9374417	0.84[ASN][1000 genomes]
rs9374420	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9387167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9400656	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9400653	GPR6	cis	cerebellum	SCAN
rs9400653	RPF2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113982400-113993600	Weak transcription	Placenta	Placenta
2	chr6:113983000-113993800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:113984200-113993200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:113984600-113993800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:113989400-113992600	Enhancers	Fetal Lung	lung
6	chr6:113989400-113993400	Enhancers	GM12878-XiMat	blood
7	chr6:113989400-113993600	Enhancers	HepG2	liver
8	chr6:113989800-113991200	Enhancers	Adipose Nuclei	Adipose
9	chr6:113990000-113993800	Weak transcription	Fetal Kidney	kidney
10	chr6:113990200-113991200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:113990200-113995600	Enhancers	Fetal Stomach	stomach
12	chr6:113990400-113991200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:113990400-113991400	Enhancers	Fetal Muscle Leg	muscle
14	chr6:113990400-113993600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:113990400-113997200	Weak transcription	Fetal Intestine Large	intestine
16	chr6:113990600-113991200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:113990600-113991400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:113990600-113993800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:113990800-113991200	Enhancers	Lung	lung
20	chr6:113990800-113991200	Enhancers	Ovary	ovary
21	chr6:113990800-113991200	Enhancers	Psoas Muscle	Psoas
22	chr6:113990800-113991200	Enhancers	Small Intestine	intestine
23	chr6:113990800-113992400	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:113990800-113993800	Weak transcription	Stomach Mucosa	stomach
25	chr6:113991000-113991200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:113991000-113991200	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr6:113991000-113991600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:113991000-113992000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:113991000-113992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:113991000-113992600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:113991000-113992600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:113991000-113992600	Weak transcription	Fetal Intestine Small	intestine
33	chr6:113991000-113992800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:113991000-113992800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:113991000-113993600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:113991000-113993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:113991000-113993800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:113991000-113994000	Weak transcription	Pancreas	Pancrea
39	chr6:113991000-113994000	Weak transcription	A549	lung

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