Variant report

Variant	rs9462054
Chromosome Location	chr6:35112394-35112395
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35107375..35109588-chr6:35112053..35114587,2	K562	blood:
2	chr6:35111770..35114566-chr6:35142353..35144098,2	MCF-7	breast:
3	chr6:35111236..35113031-chr6:35124115..35126348,2	K562	blood:

Variant related genes	Relation type
ENSG00000124678	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1093986	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11552398	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196771	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203612	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13206654	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13207848	0.80[EUR][1000 genomes]
rs13208078	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13214114	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13216424	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13219307	0.81[ASN][1000 genomes]
rs16871749	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16871809	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16871814	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896559	0.86[ASN][1000 genomes]
rs1747516	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1747517	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17610836	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17611877	0.97[ASN][1000 genomes]
rs2177382	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234044	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2395608	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494098	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2762336	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820225	0.84[ASN][1000 genomes]
rs34069418	0.86[ASN][1000 genomes]
rs34103100	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34208177	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34250961	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34715060	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34930033	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35095464	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35106671	0.80[EUR][1000 genomes]
rs35693439	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756856	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270050	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4628094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57111149	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66579470	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67167177	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67638810	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67941146	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6899618	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906666	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913286	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913975	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926532	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936337	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942104	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728238	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72896254	0.86[ASN][1000 genomes]
rs72897804	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72901705	0.98[ASN][1000 genomes]
rs7766770	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767073	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820061	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820062	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820063	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820065	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820066	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820067	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820069	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs820072	0.86[ASN][1000 genomes]
rs820083	0.83[ASN][1000 genomes]
rs820095	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs820099	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820100	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820101	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs820103	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs843937	0.86[ASN][1000 genomes]
rs9462053	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9462054	TCP11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35104400-35114000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:35106000-35113600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:35106200-35113400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:35108200-35113600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:35108200-35113800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:35108200-35113800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:35108200-35114400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:35108200-35114600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:35109200-35113600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:35109200-35114000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:35110200-35117000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:35110600-35116000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:35110600-35116000	Weak transcription	HSMMtube	muscle
14	chr6:35110800-35113400	Weak transcription	Fetal Stomach	stomach
15	chr6:35110800-35116000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:35111000-35115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:35111200-35113600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:35111200-35113800	Weak transcription	NHDF-Ad	bronchial
19	chr6:35111200-35115800	Weak transcription	HSMM	muscle
20	chr6:35111400-35113800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:35111400-35113800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:35111400-35113800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:35111400-35113800	Weak transcription	Osteobl	bone
24	chr6:35111400-35114000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:35111400-35114000	Weak transcription	Fetal Kidney	kidney
26	chr6:35111400-35116000	Weak transcription	A549	lung

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