Variant report

Variant	rs2964573
Chromosome Location	chr5:151160122-151160123
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:151038196..151041109-chr5:151157655..151161626,4	K562	blood:
2	chr5:151136346..151138979-chr5:151159171..151161654,2	MCF-7	breast:
3	chr5:151157780..151160466-chr5:151195592..151198103,2	K562	blood:
4	chr5:151159853..151162706-chr5:151286584..151288343,2	K562	blood:
5	chr5:151159444..151163789-chr5:151168224..151172241,5	K562	blood:

Variant related genes	Relation type
ENSG00000177556	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10044368	0.81[ASN][1000 genomes]
rs10075101	0.81[ASN][1000 genomes]
rs1042877	0.82[ASN][1000 genomes]
rs1062177	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875569	0.82[ASN][1000 genomes]
rs12515762	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12654573	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12654877	0.82[ASN][1000 genomes]
rs1433041	0.81[ASN][1000 genomes]
rs1549920	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549921	0.82[ASN][1000 genomes]
rs17741826	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17804178	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972780	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1978710	0.84[ASN][1000 genomes]
rs2016409	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053063	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347596	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347597	0.82[ASN][1000 genomes]
rs2915815	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915816	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2915817	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915818	0.94[ASN][1000 genomes]
rs2915820	0.91[ASN][1000 genomes]
rs2915822	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915826	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915827	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915828	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915829	0.81[ASN][1000 genomes]
rs2915868	0.82[ASN][1000 genomes]
rs2915869	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915870	0.82[ASN][1000 genomes]
rs2915871	0.82[ASN][1000 genomes]
rs2915872	0.83[ASN][1000 genomes]
rs2915873	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2915876	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915877	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915878	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915879	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915880	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915881	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915882	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915883	0.81[ASN][1000 genomes]
rs2915887	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915888	0.82[ASN][1000 genomes]
rs2915890	0.82[ASN][1000 genomes]
rs2915891	0.82[ASN][1000 genomes]
rs2915892	0.82[ASN][1000 genomes]
rs2915893	0.82[ASN][1000 genomes]
rs2915894	0.82[ASN][1000 genomes]
rs2964570	0.82[ASN][1000 genomes]
rs2964571	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964572	0.82[ASN][1000 genomes]
rs2964574	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964576	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964578	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964580	0.82[ASN][1000 genomes]
rs2964581	0.82[ASN][1000 genomes]
rs2964582	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964583	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964584	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964585	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964587	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964588	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964589	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964590	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964591	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964592	0.82[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	0.82[ASN][1000 genomes]
rs2964611	0.83[ASN][1000 genomes]
rs2964612	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964613	0.85[ASN][1000 genomes]
rs4472253	0.81[ASN][1000 genomes]
rs4571461	0.81[ASN][1000 genomes]
rs4629586	0.82[ASN][1000 genomes]
rs62377931	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62377945	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6579897	0.87[ASN][1000 genomes]
rs6579901	0.90[ASN][1000 genomes]
rs6878198	0.84[ASN][1000 genomes]
rs6879461	0.82[ASN][1000 genomes]
rs6890099	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72802204	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7720579	0.82[ASN][1000 genomes]
rs7734314	0.82[ASN][1000 genomes]
rs892005	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs892006	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs973529	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2964573	RP11-54C4.1	cis	Thyroid	GTEx
rs2964573	RP11-54C4.1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151152800-151163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:151153000-151167400	Weak transcription	Esophagus	oesophagus
3	chr5:151153000-151167400	Weak transcription	Lung	lung
4	chr5:151153000-151167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:151153800-151160400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:151153800-151162000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr5:151153800-151165200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr5:151153800-151166800	Weak transcription	Colonic Mucosa	Colon
9	chr5:151153800-151167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:151153800-151169800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:151154400-151168800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:151154400-151169000	Weak transcription	HSMMtube	muscle
13	chr5:151154600-151168800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:151154800-151165000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:151155200-151160600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr5:151155200-151163600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:151155200-151167600	Weak transcription	Spleen	Spleen
18	chr5:151155400-151160600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:151155800-151163800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:151155800-151167400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:151155800-151172200	Weak transcription	Aorta	Aorta
22	chr5:151155800-151177000	Weak transcription	Fetal Brain Male	brain
23	chr5:151156200-151166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:151156200-151167800	Weak transcription	Brain Germinal Matrix	brain
25	chr5:151156600-151160800	Weak transcription	Adipose Nuclei	Adipose
26	chr5:151156800-151160800	Weak transcription	Brain Substantia Nigra	brain
27	chr5:151156800-151166800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:151156800-151168200	Weak transcription	NHLF	lung
29	chr5:151157000-151165800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:151157200-151166200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:151157400-151160800	Weak transcription	Brain Angular Gyrus	brain
32	chr5:151157400-151161000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:151157400-151167200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:151157600-151163400	Weak transcription	Small Intestine	intestine
35	chr5:151157600-151165200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr5:151157800-151161000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:151157800-151161800	Weak transcription	NH-A	brain
38	chr5:151157800-151164000	Weak transcription	Fetal Kidney	kidney
39	chr5:151157800-151166000	Weak transcription	Thymus	Thymus
40	chr5:151158000-151160600	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:151158000-151160800	Weak transcription	NHDF-Ad	bronchial
42	chr5:151158000-151161000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:151158000-151161600	Genic enhancers	Dnd41	blood
44	chr5:151158000-151162000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:151158000-151163600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:151158000-151164400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:151158000-151165800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr5:151158000-151167200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:151158000-151168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:151158200-151160400	Genic enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links