Variant report

Variant	rs1124769
Chromosome Location	chr15:51352249-51352250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51336160..51337856-chr15:51350773..51353187,2	K562	blood:
2	chr15:51349722..51354201-chr15:51354203..51357915,5	MCF-7	breast:
3	chr15:51349609..51352321-chr2:70173142..70175096,2	MCF-7	breast:
4	chr15:51345843..51348336-chr15:51351397..51353692,2	K562	blood:
5	chr15:51343342..51345748-chr15:51350368..51352684,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1009882	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10851493	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851494	0.85[CHB][hapmap]
rs11070822	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11070831	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070832	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070833	0.90[ASN][1000 genomes]
rs11070834	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1135397	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[ASN][1000 genomes]
rs1147132	0.81[ASN][1000 genomes]
rs1147134	0.81[ASN][1000 genomes]
rs1147138	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs12440387	0.84[ASN][1000 genomes]
rs12440745	0.83[ASN][1000 genomes]
rs12442459	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443062	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591434	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591500	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591735	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12592941	0.84[ASN][1000 genomes]
rs12593342	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12593764	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593765	0.84[ASN][1000 genomes]
rs12593778	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs12593829	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12595526	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[ASN][1000 genomes]
rs12595551	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595600	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1276856	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs12900777	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1290084	0.82[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs12902649	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12909470	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12909687	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12909760	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs12909839	0.89[ASN][1000 genomes]
rs12911168	0.84[ASN][1000 genomes]
rs12912106	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12914185	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916845	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12917492	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1318765	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17646461	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs17646917	0.89[ASN][1000 genomes]
rs17647040	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17703435	0.96[ASN][1000 genomes]
rs17703518	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1871460	0.83[ASN][1000 genomes]
rs1876784	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1904430	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1955	0.83[ASN][1000 genomes]
rs2289304	0.89[ASN][1000 genomes]
rs2291107	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[ASN][1000 genomes]
rs2614768	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2614774	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2614787	0.83[ASN][1000 genomes]
rs2614788	0.83[ASN][1000 genomes]
rs2614793	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2619689	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[ASN][1000 genomes]
rs2619690	0.81[ASN][1000 genomes]
rs2619692	0.81[ASN][1000 genomes]
rs2663531	0.83[ASN][1000 genomes]
rs2663532	0.81[ASN][1000 genomes]
rs2663533	0.80[CHD][hapmap]
rs2663536	0.83[ASN][1000 genomes]
rs2663540	0.83[ASN][1000 genomes]
rs2663542	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs2663557	0.83[ASN][1000 genomes]
rs34013374	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35111245	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35372376	0.96[ASN][1000 genomes]
rs35551186	0.96[ASN][1000 genomes]
rs35573737	0.83[ASN][1000 genomes]
rs36004063	0.81[ASN][1000 genomes]
rs3784301	0.81[CHD][hapmap]
rs3784304	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[ASN][1000 genomes]
rs3825797	0.83[ASN][1000 genomes]
rs3825798	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[ASN][1000 genomes]
rs4142324	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4304967	0.84[ASN][1000 genomes]
rs4598846	0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs56036336	0.84[ASN][1000 genomes]
rs57324163	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67889301	0.85[ASN][1000 genomes]
rs7170302	0.83[ASN][1000 genomes]
rs7170310	0.81[ASN][1000 genomes]
rs7170455	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177664	0.95[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs7181201	0.81[CHD][hapmap]
rs72727114	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72727115	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8043017	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs8182062	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs936482	1.00[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cognitive performance	20125193	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1124769	SHC4	cis	cerebellum	SCAN
rs1124769	LYSMD2	cis	parietal	SCAN
rs1124769	TRPM7	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51340200-51352800	Weak transcription	Brain Anterior Caudate	brain
2	chr15:51344600-51384400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:51344800-51353600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:51344800-51366800	Weak transcription	Right Ventricle	heart
5	chr15:51345400-51357000	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:51348400-51359000	Weak transcription	Fetal Stomach	stomach
7	chr15:51348400-51360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:51348400-51366400	Weak transcription	Aorta	Aorta
9	chr15:51348600-51352600	Weak transcription	HSMMtube	muscle
10	chr15:51350400-51352800	Weak transcription	Esophagus	oesophagus
11	chr15:51350400-51356800	Weak transcription	Ovary	ovary
12	chr15:51350400-51358800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:51350400-51358800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:51350400-51366600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:51350400-51366800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:51350400-51367600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:51350600-51352400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:51350600-51369600	Weak transcription	HUVEC	blood vessel
19	chr15:51350800-51352400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:51350800-51353000	Enhancers	HepG2	liver
21	chr15:51350800-51359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:51351200-51352400	Weak transcription	HSMM	muscle
23	chr15:51351600-51353000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:51351800-51353000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:51352000-51352400	Enhancers	Brain Substantia Nigra	brain
26	chr15:51352000-51352600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:51352000-51353000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:51352000-51353600	Enhancers	Spleen	Spleen
29	chr15:51352200-51352400	Enhancers	Brain Hippocampus Middle	brain
30	chr15:51352200-51352600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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