Variant report

Variant	rs7849453
Chromosome Location	chr9:118286410-118286411
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	chr9:117988097..117989116-chr9:118286127..118287416,14	MCF-7	breast:
2	chr9:117988130..117988677-chr9:118286316..118287411,4	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10124685	0.89[JPT][hapmap]
rs10817758	0.83[JPT][hapmap]
rs10982719	0.83[JPT][hapmap]
rs10982724	0.83[JPT][hapmap]
rs10982725	0.83[JPT][hapmap]
rs2188048	0.95[ASN][1000 genomes]
rs2188066	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34976516	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3750505	0.83[JPT][hapmap]
rs4979548	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478177	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6478178	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6478179	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs689566	0.95[ASN][1000 genomes]
rs7470135	0.91[EUR][1000 genomes]
rs7848629	0.97[ASN][1000 genomes]
rs7859870	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7860046	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7860907	0.95[ASN][1000 genomes]
rs7864886	0.95[ASN][1000 genomes]
rs7865558	0.95[ASN][1000 genomes]
rs7868506	0.95[ASN][1000 genomes]
rs7869139	0.95[ASN][1000 genomes]
rs7871020	0.92[ASN][1000 genomes]
rs9299225	0.95[ASN][1000 genomes]
rs9299226	0.94[ASN][1000 genomes]
rs9299228	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9408863	0.88[JPT][hapmap]
rs9408864	0.83[JPT][hapmap]
rs9408870	0.94[ASN][1000 genomes]
rs9409148	1.00[JPT][hapmap]
rs9409149	0.83[JPT][hapmap]
rs9409166	0.93[ASN][1000 genomes]
rs9919008	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1042957	chr9:118153824-118313540	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1046948	chr9:118185587-118926891	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916622	chr9:118206309-118952390	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv540207	chr9:118206311-118920304	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv491661	chr9:118206312-118802177	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893770	chr9:118213502-118299750	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv893771	chr9:118244107-118332688	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv615252	chr9:118253001-118314667	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1043001	chr9:118253881-118333900	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv831698	chr9:118284259-118446456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7849453	C9orf29	cis	parietal	SCAN
rs7849453	ZNF618	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118276600-118286600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:118277000-118292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr9:118277200-118286600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:118277200-118286600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:118279600-118286600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:118279600-118286600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:118280800-118286600	Weak transcription	Fetal Stomach	stomach
8	chr9:118281600-118286600	Weak transcription	NHDF-Ad	bronchial
9	chr9:118282800-118286800	Enhancers	Fetal Muscle Leg	muscle
10	chr9:118283200-118286600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:118283200-118286600	Weak transcription	Aorta	Aorta
12	chr9:118283200-118291200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:118283600-118286600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:118284400-118288000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:118285200-118289200	Enhancers	Fetal Lung	lung
16	chr9:118285400-118314600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:118286000-118288400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:118286400-118286600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:118286400-118286600	Enhancers	Stomach Smooth Muscle	stomach
20	chr9:118286400-118286600	Enhancers	Osteobl	bone
21	chr9:118286400-118286800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr9:118286400-118286800	Enhancers	Fetal Kidney	kidney
23	chr9:118286400-118287200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:118286400-118288000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:118286400-118288400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:118286400-118288400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:118286400-118288400	Enhancers	Rectal Smooth Muscle	rectum
28	chr9:118286400-118289200	Enhancers	Colon Smooth Muscle	Colon
29	chr9:118286400-118289200	Enhancers	Duodenum Smooth Muscle	Duodenum

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