Variant report

Variant	rs3743496
Chromosome Location	chr15:73614408-73614409
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	chr15:73613904..73616034-chr15:73833950..73836830,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1017808	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10518997	1.00[YRI][hapmap]
rs11072407	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11072408	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11072411	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072412	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072415	0.85[ASN][1000 genomes]
rs1119251	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11634045	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11636981	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12439852	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12440576	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591304	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12594776	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12901272	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1382782	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1564347	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16957683	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1878940	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061890	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2252725	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs2292915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2415145	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2415146	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2660821	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2660824	0.81[JPT][hapmap]
rs2680338	0.84[ASN][1000 genomes]
rs2680340	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2680341	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34456824	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34953385	0.83[AFR][1000 genomes]
rs35348961	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35391014	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35608416	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35778649	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36072085	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3784795	0.89[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3859014	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3859015	1.00[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs472681	0.91[ASN][1000 genomes]
rs476846	0.85[ASN][1000 genomes]
rs4776631	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777592	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs486267	0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs488156	0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs489531	0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs491742	0.83[ASN][1000 genomes]
rs492362	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs498005	0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs498868	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs519946	0.85[ASN][1000 genomes]
rs519970	0.85[ASN][1000 genomes]
rs520824	0.81[ASN][1000 genomes]
rs549253	0.81[ASN][1000 genomes]
rs559260	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs563076	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs564765	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs568435	0.85[ASN][1000 genomes]
rs569532	0.84[ASN][1000 genomes]
rs570001	0.92[ASN][1000 genomes]
rs573397	0.85[ASN][1000 genomes]
rs576813	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs59628124	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62015498	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495057	0.89[ASW][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs7168555	0.80[AFR][1000 genomes]
rs72741448	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv457202	chr15:73612377-73680301	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv569949	chr15:73612377-73680301	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv524049	chr15:73612833-73680301	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3743496	STOML1	cis	parietal	SCAN
rs3743496	TBC1D21	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73596800-73616800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr15:73598200-73622800	Weak transcription	Right Atrium	heart
3	chr15:73598800-73620000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:73601000-73617800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:73601600-73615600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:73611000-73620200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:73611400-73622200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:73612000-73615400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:73612000-73615800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:73612000-73617400	Weak transcription	Fetal Heart	heart
11	chr15:73612000-73618000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:73612000-73620200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:73612200-73614800	Weak transcription	Fetal Brain Female	brain
14	chr15:73612200-73623200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:73612400-73616600	Weak transcription	Fetal Intestine Small	intestine
16	chr15:73612400-73618400	Weak transcription	Brain Germinal Matrix	brain
17	chr15:73612400-73620200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:73612400-73623000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:73612600-73615400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:73612600-73617200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:73613400-73615000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:73613600-73616200	Strong transcription	Right Ventricle	heart
23	chr15:73614000-73614600	Enhancers	Fetal Brain Male	brain
24	chr15:73614000-73618600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:73614200-73614600	Enhancers	Fetal Muscle Leg	muscle
26	chr15:73614200-73615000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:73614200-73615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:73614400-73615200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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