Variant report

Variant	rs2964584
Chromosome Location	chr5:151142878-151142879
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	chr5:151141912..151146351-chr5:151146659..151152863,9	MCF-7	breast:
2	chr5:151135770..151140060-chr5:151140703..151143772,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177556	Chromatin interaction
ENSG00000145907	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10044368	0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs10075101	0.80[ASN][1000 genomes]
rs1042877	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs1062177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875569	0.84[ASN][1000 genomes]
rs12108921	0.87[CHB][hapmap]
rs12109022	0.87[CHB][hapmap]
rs12515762	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12522670	0.84[CEU][hapmap]
rs12654573	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12654877	0.81[ASN][1000 genomes]
rs1433041	0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs1549920	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549921	0.85[ASN][1000 genomes]
rs17741826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17804178	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972780	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978710	0.83[ASN][1000 genomes]
rs2016409	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053063	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347596	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347597	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2913889	0.87[CHB][hapmap]
rs2913892	0.87[CHB][hapmap]
rs2913893	0.87[CHB][hapmap]
rs2913894	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2915815	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915816	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2915817	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915818	0.97[ASN][1000 genomes]
rs2915820	0.93[ASN][1000 genomes]
rs2915822	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915823	0.82[ASN][1000 genomes]
rs2915824	0.82[ASN][1000 genomes]
rs2915826	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915827	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915828	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915829	0.81[ASN][1000 genomes]
rs2915868	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2915869	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915870	0.81[ASN][1000 genomes]
rs2915871	0.82[ASN][1000 genomes]
rs2915872	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs2915873	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915874	0.82[ASN][1000 genomes]
rs2915876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915877	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915881	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915882	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915883	0.84[ASN][1000 genomes]
rs2915886	0.88[CHB][hapmap]
rs2915887	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915888	0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2915890	0.93[CHB][hapmap];0.82[JPT][hapmap];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	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2964571	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964572	0.81[ASN][1000 genomes]
rs2964573	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964574	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964576	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964577	0.82[ASN][1000 genomes]
rs2964578	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964580	0.85[ASN][1000 genomes]
rs2964581	0.85[ASN][1000 genomes]
rs2964582	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964583	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964585	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964587	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964588	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964589	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964590	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964591	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964592	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[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	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964613	0.84[ASN][1000 genomes]
rs4472253	0.80[ASN][1000 genomes]
rs4571461	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs4629586	0.81[ASN][1000 genomes]
rs62377931	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62377945	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6579897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6579901	0.92[ASN][1000 genomes]
rs6878198	0.87[ASN][1000 genomes]
rs6879461	0.81[ASN][1000 genomes]
rs6890099	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72802204	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7719617	0.94[CHB][hapmap]
rs7720579	0.81[ASN][1000 genomes]
rs7728956	0.85[CHB][hapmap]
rs7733241	0.87[CHB][hapmap]
rs7734314	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs892005	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973529	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2964584	RP11-54C4.1	cis	Thyroid	GTEx
rs2964584	CD74	cis	cerebellum	SCAN
rs2964584	C5orf46	cis	parietal	SCAN
rs2964584	RP11-54C4.1	cis	Nerve Tibial	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151138800-151149600	Weak transcription	Aorta	Aorta
2	chr5:151138800-151149800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:151139000-151148800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:151139200-151147600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:151139200-151149600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:151139400-151143000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:151139400-151145400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:151139400-151147400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:151139400-151148000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:151139400-151149800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:151139400-151149800	Weak transcription	Right Atrium	heart
12	chr5:151142600-151143000	Enhancers	K562	blood
13	chr5:151142600-151143200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:151142800-151143000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr5:151142800-151143000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:151142800-151143000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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