Variant report

Variant	rs12685091
Chromosome Location	chr9:96104237-96104238
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96102610..96104810-chr9:96126925..96128745,2	MCF-7	breast:
2	chr9:96102856..96105406-chr9:96141051..96143168,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10761210	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10761211	0.96[ASN][1000 genomes]
rs10761216	0.84[ASN][1000 genomes]
rs10761217	0.84[ASN][1000 genomes]
rs10821107	0.80[CHB][hapmap]
rs10821109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821118	0.82[ASN][1000 genomes]
rs10992701	0.90[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap]
rs10992708	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992709	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992711	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10992713	0.84[ASN][1000 genomes]
rs11789033	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs12235484	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12347460	0.81[ASN][1000 genomes]
rs2086105	0.83[ASN][1000 genomes]
rs2841680	0.83[CEU][hapmap]
rs2841681	0.83[CEU][hapmap]
rs2991377	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs2991384	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995992	0.85[ASN][1000 genomes]
rs2995995	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2995996	0.82[ASN][1000 genomes]
rs2995997	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs2995998	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs3933798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62574460	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7041850	0.83[ASN][1000 genomes]
rs7042763	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1798245	chr9:96098930-96120432	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12685091	GADD45G	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96098600-96108000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:96098800-96105000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr9:96101400-96107200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:96102600-96106000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:96102600-96107600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:96102800-96104800	Weak transcription	Gastric	stomach
7	chr9:96102800-96105800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:96102800-96106000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:96102800-96106000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:96102800-96106200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:96102800-96107200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:96102800-96107800	Weak transcription	Fetal Brain Male	brain
13	chr9:96102800-96108200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:96103000-96106000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:96103200-96104600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:96103200-96106200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:96103400-96106000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:96104000-96104400	Enhancers	Placenta	Placenta

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