Variant report

Variant	rs34487006
Chromosome Location	chr15:72462350-72462351
allele	G/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	RFX5	chr15:72462313-72462421	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72445875..72448342-chr15:72461656..72463455,2	MCF-7	breast:
2	chr15:72459257..72462704-chr15:72465780..72468461,3	MCF-7	breast:

Variant related genes	Relation type
GRAMD2	TF binding region
ENSG00000175318	Chromatin interaction
ENSG00000260173	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1037680	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10518979	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1074330	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072338	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072339	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072346	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072351	0.88[ASN][1000 genomes]
rs11852789	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11853101	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11853268	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11858015	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12050895	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12439900	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442886	0.84[ASN][1000 genomes]
rs12591313	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12591338	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12591426	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592044	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592364	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593134	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593908	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595228	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12595464	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12898585	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901580	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901886	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902006	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902661	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12903484	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906711	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12908300	0.82[EUR][1000 genomes]
rs12908882	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911154	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914070	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916694	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916951	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12917428	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1384007	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16953769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16956444	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16956452	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956634	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2035379	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2200056	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279283	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2306488	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306490	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415130	0.85[AMR][1000 genomes]
rs2607090	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856929	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2912231	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34137768	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34189331	0.83[ASN][1000 genomes]
rs35112434	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35115747	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35167572	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35186252	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35206011	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35258998	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35673773	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35713471	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743224	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803471	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4131630	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4238449	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4411469	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4445848	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776581	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4776584	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4776586	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4776589	0.87[ASN][1000 genomes]
rs4777471	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777474	0.82[ASN][1000 genomes]
rs4777477	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4777478	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4777480	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777484	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4777489	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55854204	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60921026	0.97[ASN][1000 genomes]
rs62025574	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs713048	0.83[EUR][1000 genomes]
rs71395051	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7170461	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7170754	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172309	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182776	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7183196	0.83[EUR][1000 genomes]
rs7183749	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72733369	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023703	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025504	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028532	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032038	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8192364	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8192386	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8192431	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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
rs34487006	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:72458600-72463600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr15:72459600-72462600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:72459800-72462400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:72459800-72463400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:72460000-72463400	Enhancers	Fetal Intestine Large	intestine
8	chr15:72460400-72462400	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:72460800-72462600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:72460800-72462600	Flanking Active TSS	Placenta	Placenta
11	chr15:72461000-72462800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr15:72461000-72463200	Enhancers	Stomach Mucosa	stomach
13	chr15:72461200-72462400	Weak transcription	Gastric	stomach
14	chr15:72461200-72463600	Enhancers	Fetal Intestine Small	intestine
15	chr15:72461200-72464400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:72461400-72466800	Weak transcription	NHEK	skin
17	chr15:72461800-72466400	Weak transcription	Lung	lung
18	chr15:72462000-72462600	Bivalent Enhancer	HepG2	liver
19	chr15:72462000-72471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:72462200-72462400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr15:72462200-72462600	Flanking Active TSS	Colonic Mucosa	Colon
22	chr15:72462200-72462600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr15:72462200-72462600	Flanking Active TSS	HMEC	breast
24	chr15:72462200-72462800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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