Variant report

Variant	rs8025939
Chromosome Location	chr15:72460339-72460340
allele	A/T
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	NR2F2	chr15:72460223-72460836	MCF-7	breast:	n/a	n/a
2	CEBPB	chr15:72460297-72460798	MCF-7	breast:	n/a	chr15:72460527-72460538
3	NR2F2	chr15:72460244-72461096	MCF-7	breast:	n/a	n/a
4	GATA3	chr15:72460184-72461228	MCF-7	breast:	n/a	chr15:72460978-72460988
5	EP300	chr15:72460298-72461054	T-47D	breast:	n/a	chr15:72460977-72460986

No.	Distal block	Cell Line	Cell type
1	chr15:72454000..72456435-chr15:72458895..72460767,2	MCF-7	breast:
2	chr15:72458549..72461101-chr15:72765178..72767894,2	K562	blood:
3	chr15:72459821..72461687-chr15:72564383..72566445,2	MCF-7	breast:
4	chr15:72459257..72462704-chr15:72465780..72468461,3	MCF-7	breast:

Variant related genes	Relation type
GRAMD2	TF binding region
ENSG00000166233	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000175318	Chromatin interaction
ENSG00000137817	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1000281	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs1035744	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs10851850	0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11072349	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072350	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11630170	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11630611	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631650	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11633327	0.86[EUR][1000 genomes]
rs11634608	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634622	0.88[EUR][1000 genomes]
rs11637611	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11639282	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148078	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12442886	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481862	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16956623	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2034879	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2052713	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278987	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306489	0.81[ASN][1000 genomes]
rs2415134	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28717020	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2899775	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2899776	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929508	0.82[EUR][1000 genomes]
rs2929509	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2929510	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2929511	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2929513	0.81[EUR][1000 genomes]
rs2929517	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2929518	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2929525	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2929526	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2929527	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2929532	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2930069	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957361	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957365	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957373	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs2957724	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957728	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2957734	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957735	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957736	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957737	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2957740	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957742	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957743	0.82[AMR][1000 genomes]
rs2957745	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957746	0.86[ASN][1000 genomes]
rs2957750	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35603965	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759820	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759900	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]
rs3759902	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4454922	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4506844	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777485	0.80[ASN][1000 genomes]
rs4777489	0.84[CEU][hapmap]
rs55679065	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763892	0.88[EUR][1000 genomes]
rs59975112	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022788	0.87[EUR][1000 genomes]
rs62022789	0.87[EUR][1000 genomes]
rs6494990	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6494992	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494997	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7162299	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164780	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170456	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172158	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7175197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175373	0.82[EUR][1000 genomes]
rs7175792	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179427	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179942	0.88[EUR][1000 genomes]
rs7182776	0.85[AMR][1000 genomes]
rs7183055	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183810	0.87[EUR][1000 genomes]
rs8023703	0.80[AMR][1000 genomes]
rs8023788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027164	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027647	0.88[EUR][1000 genomes]
rs8028115	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030815	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032222	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037381	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038007	0.87[EUR][1000 genomes]
rs8040216	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040828	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8182011	0.80[ASN][1000 genomes]
rs8192362	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8025939	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448400-72460800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:72448600-72460800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:72448600-72460800	Weak transcription	Right Atrium	heart
4	chr15:72448800-72460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:72449200-72460400	Weak transcription	Fetal Kidney	kidney
7	chr15:72449200-72462200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:72454600-72460600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:72455200-72460400	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:72456400-72460400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:72456600-72460600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:72456600-72460600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:72456600-72461000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:72456800-72460400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:72456800-72460400	Weak transcription	Fetal Brain Female	brain
17	chr15:72457800-72460600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:72457800-72462000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:72458600-72463600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:72458800-72460600	Enhancers	Fetal Lung	lung
21	chr15:72459200-72460400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr15:72459400-72461400	Enhancers	Fetal Stomach	stomach
23	chr15:72459600-72460400	Enhancers	HMEC	breast
24	chr15:72459600-72460800	Enhancers	Placenta	Placenta
25	chr15:72459600-72462600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:72459800-72461200	Genic enhancers	Fetal Intestine Small	intestine
27	chr15:72459800-72461800	Enhancers	Fetal Heart	heart
28	chr15:72459800-72462400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:72459800-72463400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:72460000-72460600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:72460000-72461000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:72460000-72461200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:72460000-72461200	Enhancers	Gastric	stomach
34	chr15:72460000-72461200	Bivalent Enhancer	HepG2	liver
35	chr15:72460000-72461400	Enhancers	NHEK	skin
36	chr15:72460000-72461800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:72460000-72461800	Enhancers	Fetal Brain Male	brain
38	chr15:72460000-72461800	Enhancers	Lung	lung
39	chr15:72460000-72463400	Enhancers	Fetal Intestine Large	intestine
40	chr15:72460200-72461000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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