Variant report

Variant	rs10072409
Chromosome Location	chr5:99869685-99869686
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:99869499-99869817	HepG2	liver:	n/a	n/a
2	RCOR1	chr5:99869652-99869790	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
FAM174A	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10035594	0.86[EUR][1000 genomes]
rs10036134	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10042987	0.86[EUR][1000 genomes]
rs10050943	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10065274	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10065426	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10065988	1.00[EUR][1000 genomes]
rs10076560	0.88[EUR][1000 genomes]
rs12719287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13355293	1.00[EUR][1000 genomes]
rs13355936	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13359645	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13361748	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13436095	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17157336	0.95[EUR][1000 genomes]
rs2035118	0.88[EUR][1000 genomes]
rs3088366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4307066	0.88[EUR][1000 genomes]
rs4995095	0.88[EUR][1000 genomes]
rs898765	0.88[EUR][1000 genomes]
rs9327193	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9327194	0.86[EUR][1000 genomes]
rs9327203	0.86[EUR][1000 genomes]
rs989981	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759359	chr5:99207674-99883371	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2757124	chr5:99424756-99883371	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv882461	chr5:99745767-99927338	Weak transcription Active TSS Enhancers Strong transcription 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	15 gene(s)	inside rSNPs	diseases
7	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1025132	chr5:99745775-99896429	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv882463	chr5:99784116-99898851	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv882464	chr5:99784116-99905367	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv882465	chr5:99784116-99927338	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99866600-99870000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:99866800-99870000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:99866800-99870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:99867400-99870000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:99867400-99870600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:99868200-99869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:99868200-99870400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:99868200-99870400	Weak transcription	NHEK	skin
9	chr5:99868800-99870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:99868800-99870600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:99869000-99870400	Weak transcription	HSMM	muscle
12	chr5:99869600-99870000	Enhancers	Dnd41	blood
13	chr5:99869600-99870200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:99869600-99870600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:99869600-99872600	Active TSS	GM12878-XiMat	blood

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