Variant report

Variant	rs10761333
Chromosome Location	chr9:97312584-97312585
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97311721..97313513-chr9:97315633..97318443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10115929	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119223	0.81[ASN][1000 genomes]
rs10119419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733753	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761331	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761336	0.85[EUR][1000 genomes]
rs10821364	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821367	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821369	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993226	0.81[ASN][1000 genomes]
rs10993241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10993242	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790263	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552009	0.86[ASN][1000 genomes]
rs2280300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679602	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2679611	0.86[ASN][1000 genomes]
rs2772013	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790404	0.82[ASN][1000 genomes]
rs2945802	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987882	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2987886	0.86[ASN][1000 genomes]
rs2987888	0.86[ASN][1000 genomes]
rs2987889	0.86[ASN][1000 genomes]
rs2993975	0.83[ASN][1000 genomes]
rs3864788	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291336	0.81[ASN][1000 genomes]
rs4744353	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479197	0.85[ASN][1000 genomes]
rs488270	0.92[ASN][1000 genomes]
rs491123	0.86[ASN][1000 genomes]
rs504644	0.86[ASN][1000 genomes]
rs514222	0.95[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs518768	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540124	0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543698	0.92[ASN][1000 genomes]
rs543731	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547693	0.84[ASN][1000 genomes]
rs549615	0.86[ASN][1000 genomes]
rs572689	0.86[ASN][1000 genomes]
rs573371	0.86[ASN][1000 genomes]
rs573847	0.92[ASN][1000 genomes]
rs576745	0.85[JPT][hapmap]
rs605323	0.86[ASN][1000 genomes]
rs606207	0.84[ASN][1000 genomes]
rs607160	0.86[ASN][1000 genomes]
rs6479554	0.81[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs652867	0.86[ASN][1000 genomes]
rs663092	0.86[ASN][1000 genomes]
rs669113	0.81[ASN][1000 genomes]
rs678363	0.86[ASN][1000 genomes]
rs688843	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693399	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7024700	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7048277	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781650	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867912	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs802918	0.81[CHB][hapmap]
rs802919	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409801	0.86[ASN][1000 genomes]
rs965474	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9696774	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv525298	chr9:97289583-97312584	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv972786	chr9:97308737-97320211	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10761333	HIATL1	cis	parietal	SCAN
rs10761333	PHF2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97296400-97314200	Weak transcription	Liver	Liver
2	chr9:97297200-97315000	Weak transcription	HepG2	liver
3	chr9:97302600-97315000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:97304800-97315200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:97310600-97312600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:97311600-97315200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:97312000-97313600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:97312000-97315600	Weak transcription	A549	lung
9	chr9:97312400-97313800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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