Variant report

Variant	rs2913894
Chromosome Location	chr5:151259975-151259976
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr5:151259784-151260350	ECC-1	luminal epithelium:	n/a	n/a
2	STAT3	chr5:151259838-151260193	MCF10A-Er-Src	breast:	n/a	chr5:151260113-151260120
3	MYC	chr5:151259907-151260327	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr5:151259907-151260400	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr5:151259751-151260417	ECC-1	luminal epithelium:	n/a	n/a
6	FOS	chr5:151259915-151260312	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr5:151259895-151260307	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr5:151259745-151260394	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr5:151259786-151260349	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr5:151259866-151260318	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr5:151259776-151260257	ECC-1	luminal epithelium:	n/a	n/a
12	USF1	chr5:151259877-151260294	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr5:151259836-151260334	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr5:151259710-151260554	ECC-1	luminal epithelium:	n/a	n/a
15	SRF	chr5:151259796-151260155	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
RNA5SP198	TF binding region

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10044368	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs10050657	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10062169	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10075101	0.80[EUR][1000 genomes]
rs10078632	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10079787	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1042877	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10463320	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10476776	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10476778	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1062177	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs11167557	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11167559	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11950215	0.81[JPT][hapmap]
rs11954338	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12108921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12109022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12109585	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12518238	0.87[ASN][1000 genomes]
rs12518722	0.84[ASN][1000 genomes]
rs12653926	0.87[ASN][1000 genomes]
rs12658422	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1366238	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1428159	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1428160	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1433041	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1549920	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs17741826	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2033212	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2347597	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2913878	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2913879	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2913881	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2913882	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2913888	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2913889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2913892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2913893	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915822	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2915826	0.87[CHB][hapmap]
rs2915827	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2915868	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2915872	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs2915876	0.87[CHB][hapmap]
rs2915878	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2915879	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2915880	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2915885	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2915886	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2915888	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2915890	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2915891	0.80[EUR][1000 genomes]
rs2915892	0.80[EUR][1000 genomes]
rs2915893	0.80[EUR][1000 genomes]
rs2915894	0.80[EUR][1000 genomes]
rs2964570	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2964574	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2964584	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2964587	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2964591	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2964592	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2964596	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2964597	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964599	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964601	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964603	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964604	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964606	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964610	0.81[EUR][1000 genomes]
rs2964611	0.80[EUR][1000 genomes]
rs2964613	0.80[EUR][1000 genomes]
rs35692301	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4075273	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4076138	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4259159	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4331885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360031	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4362933	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4379180	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4419575	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4472253	0.80[EUR][1000 genomes]
rs4478307	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4510568	0.82[EUR][1000 genomes]
rs4541649	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4555782	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4571461	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs4594844	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4629583	0.82[EUR][1000 genomes]
rs4629586	0.80[EUR][1000 genomes]
rs62394144	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394146	0.84[ASN][1000 genomes]
rs62394155	0.87[ASN][1000 genomes]
rs6579897	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs6579906	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6579908	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6579909	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6863833	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6863837	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6868371	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6870491	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6878691	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6892117	0.91[ASN][1000 genomes]
rs6896518	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6896664	0.91[ASN][1000 genomes]
rs72802219	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7341167	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7702751	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711609	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711771	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7712779	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7715874	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7719617	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7720579	0.80[EUR][1000 genomes]
rs7725327	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7728956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7729026	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7734314	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs892006	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9324712	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1808837	chr5:151238149-151260215	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2913894	SYNPO	cis	parietal	SCAN
rs2913894	C5orf46	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151235200-151264200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:151259200-151260000	Enhancers	Left Ventricle	heart
3	chr5:151259400-151260400	Enhancers	Fetal Heart	heart
4	chr5:151259400-151260800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr5:151259600-151260400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr5:151259800-151260000	Enhancers	Psoas Muscle	Psoas
7	chr5:151259800-151260200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:151259800-151260200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:151259800-151260200	Enhancers	Aorta	Aorta
10	chr5:151259800-151260200	Enhancers	Fetal Stomach	stomach
11	chr5:151259800-151260200	Enhancers	HSMM	muscle
12	chr5:151259800-151261000	Enhancers	Fetal Muscle Leg	muscle

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