Variant report

Variant	rs16829102
Chromosome Location	chr3:158256128-158256129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158255471..158257626-chr3:158257738..158259258,2	MCF-7	breast:
2	chr3:158251511..158254019-chr3:158254679..158258766,4	K562	blood:
3	chr3:158256043..158258049-chr3:158360702..158362682,2	K562	blood:

Variant related genes	Relation type
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1595027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1614241	0.91[ASN][1000 genomes]
rs1656375	0.91[ASN][1000 genomes]
rs16828940	0.90[JPT][hapmap]
rs16828961	0.90[JPT][hapmap]
rs16828966	0.90[JPT][hapmap]
rs16828986	0.90[JPT][hapmap]
rs16828988	0.90[JPT][hapmap]
rs16828994	0.90[JPT][hapmap]
rs16828996	0.90[JPT][hapmap]
rs16828998	0.90[JPT][hapmap]
rs16829044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16829064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs1714520	1.00[JPT][hapmap]
rs1714522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17630607	1.00[CHB][hapmap]
rs17697458	1.00[CHB][hapmap]
rs17699103	1.00[CHB][hapmap]
rs17699324	1.00[CHB][hapmap]
rs1978780	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2196357	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs2304408	1.00[CHB][hapmap]
rs3867391	1.00[CHB][hapmap]
rs4411841	0.90[JPT][hapmap]
rs55838364	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58157740	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58251618	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60589185	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62287862	0.88[ASN][1000 genomes]
rs62287863	0.88[ASN][1000 genomes]
rs62287866	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62287867	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62287869	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62287870	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62287871	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62287872	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62287885	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62287904	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62287906	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62287931	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62289511	0.83[ASN][1000 genomes]
rs62289512	0.88[ASN][1000 genomes]
rs62289513	0.88[ASN][1000 genomes]
rs62289515	0.88[ASN][1000 genomes]
rs62289516	0.88[ASN][1000 genomes]
rs6441208	1.00[CHB][hapmap]
rs6776901	1.00[CHB][hapmap]
rs6777231	1.00[CHB][hapmap]
rs6802223	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804230	1.00[CHB][hapmap]
rs6805361	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73877215	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73877220	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610009	1.00[CHB][hapmap]
rs9820727	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16829102	LXN	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158246600-158261000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr3:158249400-158264400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:158252600-158267400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr3:158253800-158261000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:158255200-158263800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:158255600-158260600	Weak transcription	Dnd41	blood

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