Variant report

Variant	rs9489340
Chromosome Location	chr6:118645282-118645283
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	chr6:118631014..118632814-chr6:118644282..118647263,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11153727	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198458	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12202670	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169465	1.00[MEX][hapmap]
rs283058	1.00[MEX][hapmap]
rs283064	1.00[MEX][hapmap]
rs283090	1.00[MEX][hapmap]
rs430538	1.00[MEX][hapmap]
rs444666	1.00[MEX][hapmap]
rs6900071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387570	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387571	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481773	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481781	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481782	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489330	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9489332	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489339	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9489341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489347	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489350	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489363	0.89[AMR][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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv604554	chr6:118631282-118716318	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv830787	chr6:118631902-118805106	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9489340	IQCG	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118635400-118646400	Weak transcription	Right Ventricle	heart
2	chr6:118637400-118646400	Weak transcription	Left Ventricle	heart
3	chr6:118639200-118645400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:118641400-118646400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:118641400-118647800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:118641400-118648400	Weak transcription	Psoas Muscle	Psoas
7	chr6:118641800-118645400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:118641800-118646600	Weak transcription	Right Atrium	heart
9	chr6:118642200-118646600	Weak transcription	NHLF	lung
10	chr6:118642600-118645400	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:118643000-118645400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:118643200-118646400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:118643400-118646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:118644800-118645800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:118644800-118645800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr6:118644800-118645800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:118644800-118646000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:118644800-118647200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:118644800-118649000	Enhancers	Aorta	Aorta
20	chr6:118645000-118645400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:118645000-118645400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:118645000-118645600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr6:118645000-118645600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:118645000-118645800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:118645000-118645800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:118645000-118647200	Enhancers	Fetal Heart	heart

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