Variant report

Variant	rs1405184
Chromosome Location	chr15:52681377-52681378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12438578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441597	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12442531	0.81[AMR][1000 genomes]
rs12900962	0.80[ASN][1000 genomes]
rs12901814	0.89[ASN][1000 genomes]
rs1405183	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1526169	0.82[MEX][hapmap]
rs1581580	0.81[AMR][1000 genomes]
rs1669877	0.82[MEX][hapmap]
rs1724593	0.81[YRI][hapmap]
rs1724630	0.81[CHB][hapmap]
rs1965563	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1972160	0.82[MEX][hapmap]
rs2290332	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290335	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290336	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2462847	0.84[ASW][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs28533733	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3794557	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3794564	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3794565	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794566	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176600	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7176830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8030535	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8032995	0.87[ASN][1000 genomes]
rs871488	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs940970	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1405184	KIAA1370	cis	parietal	SCAN
rs1405184	MYO5A	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
3	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:52649000-52687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:52658400-52687200	Weak transcription	Small Intestine	intestine
6	chr15:52662600-52683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:52662600-52685000	Weak transcription	Psoas Muscle	Psoas
8	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
11	chr15:52667000-52682000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:52667000-52684800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:52667000-52686000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:52667000-52686600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:52667600-52684400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:52668000-52683400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:52668800-52683800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
19	chr15:52669200-52683400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr15:52671200-52682000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:52671400-52681400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:52672400-52684000	Weak transcription	Fetal Heart	heart
24	chr15:52673800-52683800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:52673800-52684800	Weak transcription	Hela-S3	cervix
26	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
28	chr15:52674800-52681400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:52675000-52686200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:52676000-52683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:52676000-52684600	Weak transcription	Osteobl	bone
33	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
34	chr15:52676200-52683400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:52676200-52686400	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:52676400-52683000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:52676400-52683200	Weak transcription	A549	lung
40	chr15:52676400-52683600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:52676400-52684000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:52676400-52684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:52676400-52685600	Weak transcription	Liver	Liver
44	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
45	chr15:52676400-52696800	Weak transcription	Dnd41	blood
46	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:52676400-52701000	Weak transcription	HMEC	breast
49	chr15:52676400-52709800	Weak transcription	NHLF	lung
50	chr15:52676400-52721400	Weak transcription	Gastric	stomach

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