Variant report

Variant	rs12654573
Chromosome Location	chr5:151207473-151207474
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:151200829..151202793-chr5:151205309..151207571,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10044368	0.87[CHB][hapmap]
rs10065313	0.83[ASN][1000 genomes]
rs1042877	0.87[CHB][hapmap]
rs10476776	0.84[ASN][1000 genomes]
rs10476778	0.86[ASN][1000 genomes]
rs1062177	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11954338	0.85[ASN][1000 genomes]
rs12108921	0.93[CHB][hapmap]
rs12109022	0.93[CHB][hapmap]
rs12515762	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518238	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518722	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12522670	0.82[CEU][hapmap]
rs12653926	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12658422	0.81[ASN][1000 genomes]
rs1346489	0.80[EUR][1000 genomes]
rs1433041	0.87[CHB][hapmap]
rs1549920	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17741826	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs17804178	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1972780	0.82[ASN][1000 genomes]
rs2016409	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2053063	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2347596	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2347597	0.87[CHB][hapmap]
rs2913889	0.93[CHB][hapmap]
rs2913892	0.93[CHB][hapmap]
rs2913893	0.93[CHB][hapmap]
rs2913894	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs2915815	0.81[ASN][1000 genomes]
rs2915817	0.81[ASN][1000 genomes]
rs2915818	0.81[ASN][1000 genomes]
rs2915822	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2915826	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2915827	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2915828	0.80[ASN][1000 genomes]
rs2915868	0.87[CHB][hapmap]
rs2915869	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2915872	0.87[CHB][hapmap]
rs2915873	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2915876	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs2915877	0.85[EUR][1000 genomes]
rs2915878	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs2915879	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2915880	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2915881	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2915882	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2915885	0.84[ASN][1000 genomes]
rs2915886	0.81[CHB][hapmap]
rs2915887	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2915888	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs2915890	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2964570	0.87[CHB][hapmap]
rs2964571	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2964573	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2964574	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2964576	0.81[EUR][1000 genomes]
rs2964578	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2964582	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2964583	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2964584	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2964585	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2964587	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2964588	0.80[ASN][1000 genomes]
rs2964589	0.80[ASN][1000 genomes]
rs2964590	0.80[ASN][1000 genomes]
rs2964591	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2964592	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2964593	0.80[ASN][1000 genomes]
rs2964612	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35692301	0.81[ASN][1000 genomes]
rs4360031	0.81[ASN][1000 genomes]
rs4362933	0.81[ASN][1000 genomes]
rs4379180	0.81[ASN][1000 genomes]
rs4419575	0.87[ASN][1000 genomes]
rs4541649	0.86[ASN][1000 genomes]
rs4555782	0.81[ASN][1000 genomes]
rs4571461	0.87[CHB][hapmap]
rs4594844	0.81[ASN][1000 genomes]
rs4629583	0.83[ASN][1000 genomes]
rs59580263	0.82[EUR][1000 genomes]
rs62377931	0.86[EUR][1000 genomes]
rs62377945	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62394144	0.81[ASN][1000 genomes]
rs62394146	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62394155	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62395861	0.82[EUR][1000 genomes]
rs6579897	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6579906	0.86[ASN][1000 genomes]
rs6579908	0.81[ASN][1000 genomes]
rs6579909	0.81[ASN][1000 genomes]
rs6884630	0.81[EUR][1000 genomes]
rs6890099	0.84[EUR][1000 genomes]
rs6892117	0.80[EUR][1000 genomes]
rs6896664	0.80[EUR][1000 genomes]
rs72802204	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7715874	0.83[ASN][1000 genomes]
rs7718936	0.85[AFR][1000 genomes]
rs7719617	0.87[CHB][hapmap]
rs7726975	0.89[AFR][1000 genomes]
rs7728956	0.92[CHB][hapmap]
rs7733241	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs7734314	0.87[CHB][hapmap]
rs892005	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs892006	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs919262	0.80[EUR][1000 genomes]
rs919263	0.80[EUR][1000 genomes]
rs973529	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12654573	RP11-54C4.1	cis	Nerve Tibial	GTEx
rs12654573	RP11-54C4.1	cis	Thyroid	GTEx
rs12654573	G3BP1	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151164000-151207600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:151179800-151208400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:151183600-151210600	Weak transcription	Lung	lung
4	chr5:151183800-151208400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:151183800-151209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:151183800-151213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:151188200-151210400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:151190400-151210400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:151192200-151208200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:151192400-151209800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:151192400-151210000	Weak transcription	Aorta	Aorta
12	chr5:151192400-151211200	Weak transcription	NHLF	lung
13	chr5:151192600-151209800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:151192800-151208400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:151192800-151209600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:151192800-151209800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:151193000-151207600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:151193000-151210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:151193200-151210600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:151193600-151211400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:151194400-151207800	Weak transcription	Primary B cells from cord blood	blood
22	chr5:151194800-151209000	Weak transcription	Brain Anterior Caudate	brain
23	chr5:151194800-151209600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:151194800-151210400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:151196600-151210400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr5:151196800-151208000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:151196800-151209400	Weak transcription	Liver	Liver
28	chr5:151196800-151211400	Weak transcription	GM12878-XiMat	blood
29	chr5:151197000-151208000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:151197000-151208200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:151197000-151211400	Weak transcription	NH-A	brain
32	chr5:151198200-151210600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:151200200-151208800	Strong transcription	A549	lung
34	chr5:151200200-151211400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:151200600-151208200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:151200600-151208600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:151200800-151208000	Weak transcription	Adipose Nuclei	Adipose
38	chr5:151202600-151208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:151203800-151210400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:151204400-151210000	Strong transcription	HSMM	muscle
41	chr5:151204800-151210000	Weak transcription	HSMMtube	muscle
42	chr5:151205600-151207800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:151205600-151208600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:151205600-151208800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:151205600-151208800	Weak transcription	Fetal Thymus	thymus
46	chr5:151205600-151210000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:151205600-151210800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:151205800-151209600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:151205800-151211200	Weak transcription	Primary T cells from cord blood	blood
50	chr5:151206000-151207800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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