Variant report

Variant	rs804904
Chromosome Location	chr16:81106944-81106945
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81105753..81107546-chr7:102111679..102113893,2	MCF-7	breast:
2	chr16:81099686..81101750-chr16:81106267..81108308,2	K562	blood:
3	chr16:81104152..81107798-chr16:81108570..81111013,4	MCF-7	breast:
4	chr16:81039722..81044457-chr16:81106699..81112118,5	MCF-7	breast:
5	chr16:81101883..81103622-chr16:81105773..81108523,2	K562	blood:
6	chr16:81067084..81072191-chr16:81106033..81112629,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103121	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000264471	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000261838	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11865207	0.95[ASN][1000 genomes]
rs12927239	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12927828	0.95[ASN][1000 genomes]
rs13185	0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2257378	0.93[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2278025	0.81[ASN][1000 genomes]
rs2549892	0.83[ASN][1000 genomes]
rs2549895	0.92[ASN][1000 genomes]
rs2549896	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs2549899	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs2602401	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs2602402	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2602404	0.94[ASN][1000 genomes]
rs2602407	0.93[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2602431	0.88[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs2873310	0.85[ASN][1000 genomes]
rs2911159	0.83[ASN][1000 genomes]
rs2970076	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs35096487	0.84[ASN][1000 genomes]
rs4889225	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4889229	0.96[ASN][1000 genomes]
rs4889230	0.96[ASN][1000 genomes]
rs7185637	0.83[ASN][1000 genomes]
rs7203546	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7206814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs804885	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs804889	0.81[GIH][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs804896	0.86[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs804902	0.99[ASN][1000 genomes]
rs804903	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs804905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052415	0.89[ASN][1000 genomes]
rs935942	0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs804904	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs804904	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs804904	LOC100329108	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81079400-81109800	Weak transcription	Brain Hippocampus Middle	brain
2	chr16:81080400-81110200	Weak transcription	Ovary	ovary
3	chr16:81093000-81109800	Weak transcription	Brain Anterior Caudate	brain
4	chr16:81095000-81109400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr16:81095600-81109800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:81095800-81110200	Weak transcription	Fetal Stomach	stomach
7	chr16:81098200-81107200	Weak transcription	Placenta	Placenta
8	chr16:81101000-81110000	Weak transcription	Fetal Brain Male	brain
9	chr16:81102000-81109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:81103600-81108000	Weak transcription	Thymus	Thymus
11	chr16:81104800-81107000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:81105600-81109400	Weak transcription	Fetal Heart	heart
13	chr16:81105800-81109400	Weak transcription	Hela-S3	cervix
14	chr16:81105800-81109600	Weak transcription	HepG2	liver
15	chr16:81105800-81109800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:81105800-81109800	Weak transcription	HMEC	breast
17	chr16:81105800-81109800	Weak transcription	NHEK	skin
18	chr16:81105800-81110000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:81105800-81110000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr16:81105800-81110000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr16:81106000-81109400	Weak transcription	K562	blood
22	chr16:81106000-81109800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:81106600-81107600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:81106600-81110200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:81106800-81107600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr16:81106800-81107800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr16:81106800-81107800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr16:81106800-81107800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr16:81106800-81108000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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