Variant report

Variant	rs4147798
Chromosome Location	chr1:94585009-94585010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94532251..94537168-chr1:94582958..94586481,4	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10493869	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493870	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10874835	0.86[CHD][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165076	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165079	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165080	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165082	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11588391	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12025221	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035820	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17111122	0.93[TSI][hapmap]
rs1931564	0.83[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1931566	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1931570	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789439	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789440	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789442	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789443	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789444	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789445	0.81[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs3827714	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147801	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147807	0.84[ASN][1000 genomes]
rs4147808	0.84[ASN][1000 genomes]
rs61784007	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61784009	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1807674	chr1:94549175-94588191	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv870932	chr1:94579053-94607607	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv871679	chr1:94579426-94598568	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv871502	chr1:94579426-94607607	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv871306	chr1:94579426-94609478	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv871210	chr1:94579426-94629643	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv523430	chr1:94582249-94591481	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4147798	TMEM56	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94564600-94591800	Weak transcription	Right Atrium	heart
2	chr1:94567400-94585400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:94580200-94587600	Enhancers	Placenta	Placenta
4	chr1:94580400-94587600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:94581000-94585200	Enhancers	Ovary	ovary
6	chr1:94581400-94585200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:94581400-94587600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:94581400-94588000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:94581600-94586200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:94581600-94588600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:94582000-94585600	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:94582200-94587400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:94583000-94585600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:94583000-94591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:94583200-94585600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:94583200-94585600	Enhancers	HepG2	liver
17	chr1:94583200-94586000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:94583600-94587600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:94583600-94587600	Enhancers	Fetal Kidney	kidney
20	chr1:94583800-94585200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:94584000-94587600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:94584200-94587000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:94584400-94585400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:94584400-94587400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:94584800-94585600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:94584800-94586200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr1:94584800-94586200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:94584800-94586200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:94584800-94587600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:94585000-94585200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:94585000-94586200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:94585000-94586200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr1:94585000-94586400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:94585000-94587000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:94585000-94587400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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