Variant report

Variant	rs2016409
Chromosome Location	chr5:151126324-151126325
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10044368	0.80[ASN][1000 genomes]
rs10075101	0.80[ASN][1000 genomes]
rs1042877	0.81[ASN][1000 genomes]
rs1062177	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875569	0.84[ASN][1000 genomes]
rs12515762	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12518722	1.00[AFR][1000 genomes]
rs12654573	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12654877	0.81[ASN][1000 genomes]
rs1433041	0.80[ASN][1000 genomes]
rs1549920	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549921	0.85[ASN][1000 genomes]
rs17741826	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17804178	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972780	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978710	0.83[ASN][1000 genomes]
rs2053063	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347596	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347597	0.81[ASN][1000 genomes]
rs2915815	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915816	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2915817	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915818	0.97[ASN][1000 genomes]
rs2915820	0.93[ASN][1000 genomes]
rs2915822	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915823	0.82[ASN][1000 genomes]
rs2915824	0.82[ASN][1000 genomes]
rs2915826	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915827	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915828	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915829	0.81[ASN][1000 genomes]
rs2915868	0.81[ASN][1000 genomes]
rs2915869	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915870	0.81[ASN][1000 genomes]
rs2915871	0.82[ASN][1000 genomes]
rs2915872	0.82[ASN][1000 genomes]
rs2915873	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915874	0.82[ASN][1000 genomes]
rs2915876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915877	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915878	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915879	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915880	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915881	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915882	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915883	0.84[ASN][1000 genomes]
rs2915887	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915888	0.81[ASN][1000 genomes]
rs2915890	0.81[ASN][1000 genomes]
rs2915891	0.81[ASN][1000 genomes]
rs2915892	0.81[ASN][1000 genomes]
rs2915893	0.81[ASN][1000 genomes]
rs2915894	0.81[ASN][1000 genomes]
rs2964570	0.81[ASN][1000 genomes]
rs2964571	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964572	0.81[ASN][1000 genomes]
rs2964573	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964574	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964576	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964577	0.82[ASN][1000 genomes]
rs2964578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964580	0.85[ASN][1000 genomes]
rs2964581	0.85[ASN][1000 genomes]
rs2964582	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964583	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964584	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964587	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964588	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964589	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964590	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964591	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964592	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964593	0.96[ASN][1000 genomes]
rs2964594	0.87[ASN][1000 genomes]
rs2964595	0.89[ASN][1000 genomes]
rs2964610	0.81[ASN][1000 genomes]
rs2964611	0.82[ASN][1000 genomes]
rs2964612	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964613	0.84[ASN][1000 genomes]
rs4472253	0.80[ASN][1000 genomes]
rs4571461	0.80[ASN][1000 genomes]
rs4629586	0.81[ASN][1000 genomes]
rs62377931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62377945	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62394146	1.00[AFR][1000 genomes]
rs62394155	1.00[AFR][1000 genomes]
rs6579897	0.89[ASN][1000 genomes]
rs6579901	0.92[ASN][1000 genomes]
rs6878198	0.87[ASN][1000 genomes]
rs6879461	0.81[ASN][1000 genomes]
rs6890099	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72802204	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7720579	0.81[ASN][1000 genomes]
rs7734314	0.81[ASN][1000 genomes]
rs892005	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892006	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973529	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2016409	RP11-54C4.1	cis	Nerve Tibial	GTEx
rs2016409	RP11-54C4.1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151120000-151137600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:151120200-151137000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:151120200-151137200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:151120600-151132400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:151120600-151135000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:151120800-151134600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:151120800-151135000	Weak transcription	Small Intestine	intestine
8	chr5:151120800-151135200	Weak transcription	Stomach Mucosa	stomach
9	chr5:151120800-151136800	Weak transcription	Ovary	ovary
10	chr5:151120800-151136800	Weak transcription	Hela-S3	cervix
11	chr5:151120800-151137000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:151121800-151126400	Strong transcription	Brain Germinal Matrix	brain
13	chr5:151121800-151126400	Genic enhancers	NHEK	skin
14	chr5:151122000-151127000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:151122600-151128800	Strong transcription	Fetal Intestine Large	intestine
16	chr5:151123400-151137200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:151123600-151126400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:151124000-151129000	Strong transcription	Fetal Intestine Small	intestine
19	chr5:151124200-151126400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr5:151124200-151126400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr5:151124200-151126400	Genic enhancers	Brain Anterior Caudate	brain
22	chr5:151124200-151126400	Genic enhancers	HMEC	breast
23	chr5:151124200-151127200	Enhancers	Brain Hippocampus Middle	brain
24	chr5:151124400-151126400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr5:151124400-151126400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr5:151124400-151126400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr5:151124400-151126400	Enhancers	Brain Angular Gyrus	brain
28	chr5:151124400-151126400	Enhancers	Brain Cingulate Gyrus	brain
29	chr5:151124400-151126600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:151124400-151127400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr5:151124400-151136200	Weak transcription	Colonic Mucosa	Colon
32	chr5:151124600-151126400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr5:151124600-151126400	Genic enhancers	Primary T cells from cord blood	blood
34	chr5:151124600-151126400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr5:151124600-151126400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:151124600-151126400	Genic enhancers	Adipose Nuclei	Adipose
37	chr5:151124600-151126400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr5:151124600-151126400	Enhancers	Fetal Heart	heart
39	chr5:151124600-151126400	Genic enhancers	Lung	lung
40	chr5:151124600-151126400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:151125000-151126800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:151125000-151136800	Weak transcription	Psoas Muscle	Psoas
43	chr5:151125200-151126400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:151125200-151127400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:151125400-151126400	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr5:151125400-151126400	Genic enhancers	Monocytes-CD14+_RO01746	blood
47	chr5:151125400-151126400	Enhancers	NHDF-Ad	bronchial
48	chr5:151125400-151129000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:151125600-151126400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:151125600-151126600	Enhancers	Primary hematopoietic stem cells	blood

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