Variant report

Variant	rs13217047
Chromosome Location	chr6:28556051-28556052
allele	C/G
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	E2F4	chr6:28555966-28556148	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28456446..28459153-chr6:28555326..28557057,2	MCF-7	breast:

Variant related genes	Relation type
SCAND3	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1005126	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs11963067	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13196606	0.85[CEU][hapmap]
rs13215054	0.88[AFR][1000 genomes]
rs16894116	0.94[CEU][hapmap]
rs16894184	0.82[ASN][1000 genomes]
rs16901847	0.94[CEU][hapmap]
rs16901848	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17336532	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394102	0.81[ASN][1000 genomes]
rs34388845	0.81[ASN][1000 genomes]
rs35051649	0.85[ASN][1000 genomes]
rs35257859	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35546888	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35778344	0.89[ASN][1000 genomes]
rs41270599	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902687	0.81[CHB][hapmap]
rs6905380	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs6923110	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6941188	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7742957	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7766356	0.94[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	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
rs13217047	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13217047	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13217047	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552400-28559600	Strong transcription	K562	blood
2	chr6:28553000-28558200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28553200-28558200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28553200-28558600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28553800-28556400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:28553800-28557600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28553800-28558200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28553800-28558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:28553800-28558400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
11	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:28554000-28558000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr6:28554400-28558400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:28554400-28558400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:28554600-28556200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:28554600-28557200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28555200-28556200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
18	chr6:28555400-28556200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr6:28555400-28556200	Flanking Active TSS	Hela-S3	cervix
20	chr6:28555400-28557200	Weak transcription	Spleen	Spleen
21	chr6:28555600-28556200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:28555600-28556200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:28555600-28556200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:28555600-28557000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:28555600-28557200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:28555600-28557400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:28555800-28556200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:28555800-28556200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:28555800-28556200	Bivalent Enhancer	Brain Hippocampus Middle	brain
30	chr6:28555800-28556200	Flanking Active TSS	NHEK	skin
31	chr6:28555800-28556400	Active TSS	HepG2	liver
32	chr6:28555800-28556600	Weak transcription	Fetal Brain Male	brain
33	chr6:28555800-28556600	Enhancers	Fetal Lung	lung
34	chr6:28555800-28556800	Bivalent Enhancer	Fetal Kidney	kidney
35	chr6:28555800-28556800	Weak transcription	NH-A	brain
36	chr6:28555800-28556800	Weak transcription	NHLF	lung
37	chr6:28555800-28557000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:28555800-28557000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:28555800-28557000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:28555800-28557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:28555800-28557200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:28555800-28557200	Weak transcription	Right Ventricle	heart
43	chr6:28555800-28557200	Enhancers	Osteobl	bone
44	chr6:28555800-28557400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:28555800-28557400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:28555800-28557400	Weak transcription	Pancreas	Pancrea
47	chr6:28556000-28556200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:28556000-28556200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr6:28556000-28556200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:28556000-28556200	Flanking Active TSS	A549	lung

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