Variant report

Variant	rs1048510
Chromosome Location	chr9:97321127-97321128
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	chr9:97315622..97318478-chr9:97321080..97323173,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10115132	0.82[YRI][hapmap]
rs10117554	0.84[AMR][1000 genomes]
rs10122208	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10123891	0.85[EUR][1000 genomes]
rs10761334	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761335	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761338	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761339	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10821368	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993237	0.80[AMR][1000 genomes]
rs10993240	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993243	0.84[EUR][1000 genomes]
rs11789810	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13299030	0.83[AMR][1000 genomes]
rs1568305	0.85[AMR][1000 genomes]
rs2406664	0.85[YRI][hapmap]
rs2406665	0.85[YRI][hapmap]
rs2406666	0.85[YRI][hapmap]
rs2772011	0.82[YRI][hapmap]
rs2945796	0.82[YRI][hapmap]
rs2945798	0.85[YRI][hapmap]
rs2987883	0.82[YRI][hapmap]
rs3802468	0.85[EUR][1000 genomes]
rs3852401	0.85[YRI][hapmap]
rs4314706	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743959	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744357	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs498533	0.82[YRI][hapmap]
rs498635	0.82[YRI][hapmap]
rs501380	0.82[YRI][hapmap]
rs509022	0.82[YRI][hapmap]
rs540236	0.85[YRI][hapmap]
rs564430	0.82[YRI][hapmap]
rs597003	0.82[YRI][hapmap]
rs598386	0.85[YRI][hapmap]
rs599229	0.82[YRI][hapmap]
rs609901	0.82[YRI][hapmap]
rs612498	0.85[YRI][hapmap]
rs612952	0.85[YRI][hapmap]
rs62578748	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs642035	0.85[YRI][hapmap]
rs642477	0.85[YRI][hapmap]
rs642952	0.85[YRI][hapmap]
rs644237	0.82[YRI][hapmap]
rs645125	0.82[YRI][hapmap]
rs660911	0.82[YRI][hapmap]
rs693122	0.82[YRI][hapmap]
rs7035381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868159	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes]
rs7868536	0.84[EUR][1000 genomes]
rs7870433	0.87[CHB][hapmap]

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	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv893595	chr9:97268182-97330693	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1048510	PHF2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97317200-97325400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:97317200-97354000	Weak transcription	Gastric	stomach
3	chr9:97317600-97325200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:97317600-97328600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:97317800-97325400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:97318200-97324400	Weak transcription	A549	lung
7	chr9:97318200-97327200	Weak transcription	Hela-S3	cervix
8	chr9:97318200-97332000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:97318600-97325400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:97318800-97321200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:97318800-97321200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:97318800-97321200	Weak transcription	HepG2	liver
13	chr9:97318800-97322400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:97318800-97326200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:97318800-97326600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:97318800-97331600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:97319200-97321600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:97319200-97321800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:97319200-97331800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:97320400-97325600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:97320800-97330600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:97321000-97322400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:97321000-97322800	Strong transcription	Liver	Liver
24	chr9:97321000-97322800	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:97321000-97325800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:97321000-97326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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