Variant report

Variant	rs4859673
Chromosome Location	chr4:77364799-77364800
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	chr4:77364531..77366134-chr4:77367327..77368970,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10031136	0.85[CEU][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11723732	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13146564	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13152154	0.80[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1398017	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1511817	0.82[GIH][hapmap]
rs1849215	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1949137	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2136854	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4241593	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859674	0.94[CEU][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532417	0.83[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6839100	0.85[EUR][1000 genomes]
rs6843293	0.85[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7660542	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757941	chr4:77264596-77417457	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759262	chr4:77264596-77455405	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4859673	ADM	trans	parietal	SCAN
rs4859673	CCDC158	cis	parietal	SCAN
rs4859673	CCDC158	cis	lung	GTEx
rs4859673	ART3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77357400-77364800	Weak transcription	Liver	Liver
2	chr4:77357400-77368000	Weak transcription	Brain Substantia Nigra	brain
3	chr4:77357400-77370600	Weak transcription	Fetal Brain Male	brain
4	chr4:77360400-77366800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:77360400-77368800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:77360400-77369400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:77360400-77371200	Weak transcription	Aorta	Aorta
8	chr4:77360800-77367000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:77361600-77367800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:77362800-77366800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:77363200-77365400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:77363600-77365800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:77363800-77364800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:77363800-77364800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:77363800-77365000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:77363800-77365000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr4:77364000-77365000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:77364000-77365000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr4:77364000-77365000	Enhancers	Fetal Heart	heart
20	chr4:77364000-77365400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:77364200-77370600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:77364400-77365000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:77364600-77365000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr4:77364600-77365000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:77364600-77368600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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