Variant report

Variant	rs3759900
Chromosome Location	chr15:72451827-72451828
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	chr15:72410298..72412761-chr15:72451442..72454163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166192	Chromatin interaction
ENSG00000066933	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1000281	0.83[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1035744	0.83[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs1037680	0.84[TSI][hapmap]
rs10851850	0.83[CEU][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072346	0.81[TSI][hapmap]
rs11072349	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072350	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11630170	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11630611	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11631650	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11633327	0.80[EUR][1000 genomes]
rs11634608	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11634622	0.83[EUR][1000 genomes]
rs11637611	0.83[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11639282	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442886	0.80[MKK][hapmap];0.82[AMR][1000 genomes]
rs12592044	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs12901886	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12902006	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12904652	0.81[TSI][hapmap]
rs12914070	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12916951	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs13858	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1481860	0.80[ASN][1000 genomes]
rs1481862	0.81[AMR][1000 genomes]
rs16956623	0.80[AMR][1000 genomes]
rs16956634	0.84[TSI][hapmap]
rs2034879	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052713	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2278987	0.94[CEU][hapmap];0.87[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2415134	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2856929	0.84[TSI][hapmap]
rs2899775	0.84[AMR][1000 genomes]
rs2899776	0.86[AMR][1000 genomes]
rs2912231	0.89[TSI][hapmap]
rs2929509	0.80[AMR][1000 genomes]
rs2929517	0.81[EUR][1000 genomes]
rs2929518	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs2929527	0.84[AMR][1000 genomes]
rs2929528	0.84[ASN][1000 genomes]
rs2929532	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2957361	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2957365	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957368	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957724	0.81[AMR][1000 genomes]
rs2957725	0.82[ASN][1000 genomes]
rs2957734	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2957735	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs2957736	0.83[AMR][1000 genomes]
rs2957737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[ASN][1000 genomes]
rs2957740	0.85[AMR][1000 genomes]
rs2957742	0.87[AMR][1000 genomes]
rs2957743	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2957745	0.84[AMR][1000 genomes]
rs2957750	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35603965	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3743224	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs3759820	0.86[AMR][1000 genomes]
rs3759902	0.86[AMR][1000 genomes]
rs4238449	0.86[CEU][hapmap]
rs4454922	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4506844	0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4776586	0.88[CEU][hapmap]
rs4777485	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55679065	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55763892	0.83[EUR][1000 genomes]
rs59975112	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62022788	0.82[EUR][1000 genomes]
rs62022789	0.82[EUR][1000 genomes]
rs6494990	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494992	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6494997	0.83[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs7162299	0.89[ASW][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7164780	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170456	0.83[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7172158	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7172309	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs7175197	0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7175792	0.89[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7179427	0.85[AMR][1000 genomes]
rs7179942	0.83[EUR][1000 genomes]
rs7182776	0.84[ASW][hapmap];0.88[CEU][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7183055	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7183810	0.82[EUR][1000 genomes]
rs8023703	0.83[AMR][1000 genomes]
rs8023788	0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025939	0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8027164	0.94[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8027647	0.84[EUR][1000 genomes]
rs8028115	0.94[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8030815	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032222	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8037381	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8038007	0.83[EUR][1000 genomes]
rs8040216	0.93[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes]
rs8040828	0.89[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8182011	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8192362	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8192386	0.87[TSI][hapmap]
rs8192431	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3759900	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs3759900	PARP6	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448400-72453000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:72448400-72458800	Weak transcription	Spleen	Spleen
3	chr15:72448400-72460800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:72448600-72453400	Weak transcription	Brain Substantia Nigra	brain
5	chr15:72448600-72453800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:72448600-72453800	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:72448600-72456200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:72448600-72458600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:72448600-72460800	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:72448600-72460800	Weak transcription	Right Atrium	heart
11	chr15:72448800-72452400	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:72448800-72453000	Weak transcription	Fetal Intestine Small	intestine
13	chr15:72448800-72453000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:72448800-72453000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:72448800-72453200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:72448800-72453200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:72448800-72453200	Weak transcription	Lung	lung
18	chr15:72448800-72453600	Weak transcription	Fetal Stomach	stomach
19	chr15:72448800-72453800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:72448800-72453800	Weak transcription	Brain Angular Gyrus	brain
21	chr15:72448800-72454200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:72448800-72454400	Weak transcription	Fetal Brain Male	brain
23	chr15:72448800-72455800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:72448800-72456000	Weak transcription	Fetal Brain Female	brain
25	chr15:72448800-72459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:72448800-72460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:72449000-72453400	Weak transcription	Brain Anterior Caudate	brain
29	chr15:72449000-72453400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:72449000-72453800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:72449000-72454800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:72449000-72456000	Weak transcription	Hela-S3	cervix
33	chr15:72449000-72459200	Weak transcription	HMEC	breast
34	chr15:72449000-72459800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:72449200-72460400	Weak transcription	Fetal Kidney	kidney
36	chr15:72449200-72462200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:72451200-72453000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:72451400-72454000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:72451600-72453200	Strong transcription	Placenta	Placenta

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