Variant report

Variant	rs3802468
Chromosome Location	chr9:97315304-97315305
allele	C/T
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	MAX	chr9:97315198-97316103	MCF-7	breast:	n/a	chr9:97316046-97316056 chr9:97315970-97315980
2	CTCF	chr9:97315288-97315896	MCF-7	breast:	n/a	n/a
3	CTCF	chr9:97315297-97315766	K562	blood:	n/a	n/a
4	RAD21	chr9:97315284-97315800	MCF-7	breast:	n/a	n/a
5	CTCF	chr9:97315271-97315750	MCF-7	breast:	n/a	n/a
6	RAD21	chr9:97315255-97315794	MCF-7	breast:	n/a	n/a
7	CTCF	chr9:97315240-97315390	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97309308..97311468-chr9:97313942..97316861,2	MCF-7	breast:
2	chr9:97314619..97316650-chr9:97365797..97368541,2	K562	blood:

Variant related genes	Relation type
PCAT7	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10122208	0.80[EUR][1000 genomes]
rs10123891	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048510	0.85[EUR][1000 genomes]
rs10761334	0.80[EUR][1000 genomes]
rs10761335	0.85[EUR][1000 genomes]
rs10761338	0.80[EUR][1000 genomes]
rs10821357	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821361	0.82[ASN][1000 genomes]
rs10821368	0.80[EUR][1000 genomes]
rs10993237	0.81[EUR][1000 genomes]
rs10993243	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11789810	0.81[EUR][1000 genomes]
rs1754432	0.82[ASN][1000 genomes]
rs1754433	0.83[ASN][1000 genomes]
rs2406664	0.83[ASN][1000 genomes]
rs2406665	0.83[ASN][1000 genomes]
rs2406666	0.83[ASN][1000 genomes]
rs2772011	0.83[ASN][1000 genomes]
rs2772012	0.83[ASN][1000 genomes]
rs2945795	0.83[ASN][1000 genomes]
rs2945798	0.83[ASN][1000 genomes]
rs2987883	0.84[ASN][1000 genomes]
rs2993963	0.84[ASN][1000 genomes]
rs478604	0.83[ASN][1000 genomes]
rs498533	0.83[ASN][1000 genomes]
rs498635	0.83[ASN][1000 genomes]
rs501380	0.83[ASN][1000 genomes]
rs509022	0.84[ASN][1000 genomes]
rs540236	0.83[ASN][1000 genomes]
rs558753	0.83[ASN][1000 genomes]
rs564430	0.83[ASN][1000 genomes]
rs586140	0.84[ASN][1000 genomes]
rs597003	0.83[ASN][1000 genomes]
rs598386	0.83[ASN][1000 genomes]
rs599229	0.83[ASN][1000 genomes]
rs609901	0.83[ASN][1000 genomes]
rs612498	0.83[ASN][1000 genomes]
rs612952	0.83[ASN][1000 genomes]
rs62578748	0.81[EUR][1000 genomes]
rs642035	0.83[ASN][1000 genomes]
rs642477	0.83[ASN][1000 genomes]
rs642952	0.83[ASN][1000 genomes]
rs644237	0.83[ASN][1000 genomes]
rs645125	0.84[ASN][1000 genomes]
rs660911	0.83[ASN][1000 genomes]
rs693122	0.83[ASN][1000 genomes]
rs7024381	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7035309	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7035381	0.85[EUR][1000 genomes]
rs7039582	0.85[EUR][1000 genomes]
rs7868536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97312000-97315600	Weak transcription	A549	lung
2	chr9:97313000-97316800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:97313200-97316600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:97313400-97315600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:97313600-97316000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:97313800-97315400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:97313800-97315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:97314200-97315400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:97314800-97315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:97314800-97315800	Enhancers	Stomach Mucosa	stomach
11	chr9:97315000-97315400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr9:97315000-97315400	Enhancers	Hela-S3	cervix
13	chr9:97315000-97316000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:97315200-97315400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:97315200-97315400	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr9:97315200-97315600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:97315200-97315600	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr9:97315200-97315600	Flanking Active TSS	HepG2	liver
19	chr9:97315200-97315800	Enhancers	Gastric	stomach
20	chr9:97315200-97315800	Enhancers	Pancreas	Pancrea
21	chr9:97315200-97316400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:97315200-97316400	Flanking Active TSS	Liver	Liver
23	chr9:97315200-97319200	Active TSS	ES-I3 Cell Line	embryonic stem cell

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