Variant report

Variant	rs13321802
Chromosome Location	chr3:156611328-156611329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156392020..156393902-chr3:156609994..156612855,2	MCF-7	breast:
2	chr3:156392366..156393969-chr3:156610650..156612474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10936040	0.84[YRI][hapmap]
rs11710516	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11717138	1.00[JPT][hapmap]
rs11927500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12634915	0.81[YRI][hapmap]
rs13322318	0.81[YRI][hapmap]
rs1430412	1.00[JPT][hapmap]
rs168248	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16826858	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16826864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16826899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16826906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16826948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs171080	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17451232	1.00[CHB][hapmap]
rs180747	1.00[CHB][hapmap]
rs182936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs184677	1.00[CHB][hapmap]
rs193198	1.00[CHB][hapmap]
rs193423	1.00[CHB][hapmap]
rs2054881	1.00[CHB][hapmap]
rs2129909	1.00[CHB][hapmap]
rs2321290	0.84[YRI][hapmap]
rs237246	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2633815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2874490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2874491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs343992	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344014	1.00[CHB][hapmap]
rs344015	1.00[CHB][hapmap]
rs344016	1.00[CHB][hapmap]
rs344017	1.00[CHB][hapmap]
rs344052	1.00[CHB][hapmap]
rs344053	1.00[CHB][hapmap]
rs344054	1.00[CHB][hapmap]
rs344055	1.00[CHB][hapmap]
rs344058	1.00[CHB][hapmap]
rs344059	1.00[CHB][hapmap]
rs344060	1.00[CHB][hapmap]
rs344061	1.00[CHB][hapmap]
rs344062	1.00[CHB][hapmap]
rs344063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344064	1.00[CHB][hapmap]
rs344065	1.00[CHB][hapmap]
rs344066	1.00[CHB][hapmap]
rs344068	1.00[CHB][hapmap]
rs344069	1.00[CHB][hapmap]
rs344070	1.00[CHB][hapmap]
rs344071	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs344072	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs344074	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs344076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs344078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs344081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs344086	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344088	1.00[JPT][hapmap]
rs344089	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs344090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344091	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344092	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs344093	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3796172	1.00[JPT][hapmap]
rs414683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs419287	1.00[CHB][hapmap]
rs427384	1.00[CHB][hapmap]
rs4429586	1.00[CHB][hapmap]
rs4441614	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs491423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55850252	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58207863	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6441099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441100	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6441103	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6441104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774702	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787535	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6787952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6792917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6795327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6795516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6802042	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6802511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7426821	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7609851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7618306	1.00[JPT][hapmap]
rs7621699	0.90[ASN][1000 genomes]
rs7630909	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7635521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7640994	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7650127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs9810194	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9823112	1.00[CHB][hapmap]
rs9841269	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9844054	0.81[YRI][hapmap]
rs9847692	1.00[JPT][hapmap]
rs9861359	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9871817	0.81[YRI][hapmap]
rs9878709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13321802	LEKR1	cis	Thyroid	GTEx
rs13321802	LEKR1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156609600-156611600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156609600-156612000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:156609800-156611400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:156610000-156611400	Enhancers	HMEC	breast
5	chr3:156610000-156611600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:156610400-156611400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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