Variant report

Variant	rs2053063
Chromosome Location	chr5:151166764-151166765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:151151210..151153371-chr5:151165047..151166781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177556	Chromatin interaction
ENSG00000145907	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10044368	0.84[ASN][1000 genomes]
rs10075101	0.84[ASN][1000 genomes]
rs1042877	0.85[ASN][1000 genomes]
rs1062177	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875569	0.82[ASN][1000 genomes]
rs12515762	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12654573	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12654877	0.85[ASN][1000 genomes]
rs1433041	0.84[ASN][1000 genomes]
rs1549920	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1549921	0.81[ASN][1000 genomes]
rs17741826	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17804178	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972780	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1978710	0.82[ASN][1000 genomes]
rs2016409	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347596	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347597	0.85[ASN][1000 genomes]
rs2915815	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915816	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2915817	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915818	0.94[ASN][1000 genomes]
rs2915820	0.91[ASN][1000 genomes]
rs2915822	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915826	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915827	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915828	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915868	0.85[ASN][1000 genomes]
rs2915869	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915870	0.85[ASN][1000 genomes]
rs2915871	0.81[ASN][1000 genomes]
rs2915872	0.83[ASN][1000 genomes]
rs2915873	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915876	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915877	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915879	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915880	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915881	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915882	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915883	0.81[ASN][1000 genomes]
rs2915887	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915888	0.85[ASN][1000 genomes]
rs2915890	0.85[ASN][1000 genomes]
rs2915891	0.85[ASN][1000 genomes]
rs2915892	0.85[ASN][1000 genomes]
rs2915893	0.85[ASN][1000 genomes]
rs2915894	0.85[ASN][1000 genomes]
rs2964568	0.83[ASN][1000 genomes]
rs2964569	0.81[ASN][1000 genomes]
rs2964570	0.85[ASN][1000 genomes]
rs2964571	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964572	0.85[ASN][1000 genomes]
rs2964573	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964574	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964576	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964578	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964580	0.81[ASN][1000 genomes]
rs2964581	0.81[ASN][1000 genomes]
rs2964582	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964583	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964584	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964585	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964587	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964588	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964589	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964590	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964591	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964592	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964593	0.93[ASN][1000 genomes]
rs2964594	0.85[ASN][1000 genomes]
rs2964595	0.87[ASN][1000 genomes]
rs2964610	0.85[ASN][1000 genomes]
rs2964611	0.86[ASN][1000 genomes]
rs2964612	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964613	0.88[ASN][1000 genomes]
rs4472253	0.84[ASN][1000 genomes]
rs4571461	0.84[ASN][1000 genomes]
rs4629586	0.85[ASN][1000 genomes]
rs62377931	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62377945	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6579897	0.87[ASN][1000 genomes]
rs6579901	0.90[ASN][1000 genomes]
rs6878198	0.84[ASN][1000 genomes]
rs6879461	0.85[ASN][1000 genomes]
rs6890099	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72802204	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720579	0.85[ASN][1000 genomes]
rs7734314	0.85[ASN][1000 genomes]
rs892005	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892006	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973529	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2053063	RP11-54C4.1	cis	Thyroid	GTEx
rs2053063	RP11-54C4.1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151153000-151167400	Weak transcription	Esophagus	oesophagus
2	chr5:151153000-151167400	Weak transcription	Lung	lung
3	chr5:151153000-151167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:151153800-151166800	Weak transcription	Colonic Mucosa	Colon
5	chr5:151153800-151167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:151153800-151169800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:151154400-151168800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:151154400-151169000	Weak transcription	HSMMtube	muscle
9	chr5:151154600-151168800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:151155200-151167600	Weak transcription	Spleen	Spleen
11	chr5:151155800-151167400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:151155800-151172200	Weak transcription	Aorta	Aorta
13	chr5:151155800-151177000	Weak transcription	Fetal Brain Male	brain
14	chr5:151156200-151167800	Weak transcription	Brain Germinal Matrix	brain
15	chr5:151156800-151166800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:151156800-151168200	Weak transcription	NHLF	lung
17	chr5:151157400-151167200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:151158000-151167200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:151158000-151168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:151158200-151167200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:151158200-151171200	Weak transcription	Right Ventricle	heart
22	chr5:151158600-151167600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:151158800-151167200	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:151158800-151167400	Weak transcription	Pancreas	Pancrea
25	chr5:151159000-151166800	Weak transcription	HMEC	breast
26	chr5:151160400-151168200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:151160400-151168200	Weak transcription	Gastric	stomach
28	chr5:151160400-151169400	Weak transcription	Right Atrium	heart
29	chr5:151161200-151166800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:151161200-151170400	Weak transcription	Brain Anterior Caudate	brain
31	chr5:151161400-151170400	Weak transcription	Brain Substantia Nigra	brain
32	chr5:151161600-151167400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:151161600-151169000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:151161600-151169000	Weak transcription	Brain Angular Gyrus	brain
35	chr5:151162200-151167600	Weak transcription	Fetal Brain Female	brain
36	chr5:151162200-151169000	Weak transcription	NHDF-Ad	bronchial
37	chr5:151163800-151167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:151164000-151169200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:151164000-151187800	Weak transcription	Stomach Mucosa	stomach
40	chr5:151164000-151196600	Strong transcription	Hela-S3	cervix
41	chr5:151164000-151207600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:151164200-151166800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:151164400-151189400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:151164400-151194800	Strong transcription	Dnd41	blood
45	chr5:151164600-151197000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:151164800-151167000	Strong transcription	K562	blood
47	chr5:151164800-151167400	Weak transcription	Fetal Kidney	kidney
48	chr5:151164800-151171200	Weak transcription	Small Intestine	intestine
49	chr5:151164800-151196600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:151164800-151196800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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