Variant report

Variant	rs16829104
Chromosome Location	chr3:158258420-158258421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158251511..158254019-chr3:158254679..158258766,4	K562	blood:
2	chr3:158257580..158259170-chr3:158289106..158290622,2	K562	blood:
3	chr3:158255471..158257626-chr3:158257738..158259258,2	MCF-7	breast:
4	chr3:158257580..158259389-chr3:158289106..158290845,2	K562	blood:
5	chr3:156877180..156879858-chr3:158256937..158259532,2	MCF-7	breast:
6	chr3:158256966..158258990-chr3:158506924..158509258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10936143	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs10936144	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10936145	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11708784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710813	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12491598	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12492884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494926	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12495085	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631704	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs1656368	0.90[ASN][1000 genomes]
rs1656369	0.90[ASN][1000 genomes]
rs17628958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17628988	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17684859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28431969	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4334688	0.87[YRI][hapmap]
rs4680441	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55720154	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55765541	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55842512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768636	0.86[YRI][hapmap]
rs6784511	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6788907	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6801874	0.87[YRI][hapmap]
rs6806967	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs73154304	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73154306	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73154307	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73154309	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154313	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73154314	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73154326	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154331	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154340	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73172114	0.81[AMR][1000 genomes]
rs73172119	0.81[AMR][1000 genomes]
rs73172134	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7613528	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7649643	0.90[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16829104	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs16829104	RSRC1	cis	normal skin	skin_eQTL
rs16829104	RP11-538P18.2	cis	Adipose Subcutaneous	GTEx
rs16829104	RSRC1	cis	Adipose Subcutaneous	GTEx
rs16829104	RP11-538P18.2	cis	Artery Tibial	GTEx
rs16829104	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs16829104	RP11-538P18.2	cis	Nerve Tibial	GTEx

Chromatin state (count:18 , 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
7	chr3:158256200-158264600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:158256600-158280000	Weak transcription	K562	blood
9	chr3:158257000-158262400	Weak transcription	Primary B cells from cord blood	blood
10	chr3:158257200-158261200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:158257400-158261200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:158257400-158262200	Weak transcription	Liver	Liver
13	chr3:158257800-158268000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:158258000-158261200	Weak transcription	Fetal Heart	heart
15	chr3:158258000-158265000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:158258000-158265000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:158258000-158268600	Weak transcription	Pancreas	Pancrea
18	chr3:158258200-158268200	Weak transcription	Adipose Nuclei	Adipose

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