Variant report

Variant	rs10124673
Chromosome Location	chr9:118286802-118286803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117443932..117444479-chr9:118286459..118287036,2	MCF-7	breast:
2	chr9:117988097..117989116-chr9:118286127..118287416,14	MCF-7	breast:
3	chr9:117988130..117988677-chr9:118286316..118287411,4	MCF-7	breast:
4	chr9:117776404..117777930-chr9:118286444..118287425,4	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1006008	0.86[EUR][1000 genomes]
rs10116519	0.86[EUR][1000 genomes]
rs10123924	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817790	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817791	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817792	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817802	0.84[EUR][1000 genomes]
rs10982789	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10982791	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10982846	0.86[EUR][1000 genomes]
rs11999332	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12342529	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2027929	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2188052	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2188053	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2188067	0.84[EUR][1000 genomes]
rs2418367	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2418393	0.86[EUR][1000 genomes]
rs3899074	0.86[EUR][1000 genomes]
rs4246911	0.86[EUR][1000 genomes]
rs4979549	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4979550	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4979551	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979569	0.86[EUR][1000 genomes]
rs4997383	0.86[EUR][1000 genomes]
rs6478180	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478181	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478182	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478183	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6478184	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6478185	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6478196	0.86[EUR][1000 genomes]
rs7024456	0.87[EUR][1000 genomes]
rs7026805	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7027022	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7029913	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7030481	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7033287	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7046356	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs718019	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7466595	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7466771	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7467026	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7467728	0.84[EUR][1000 genomes]
rs7468290	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7469165	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7469418	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7469817	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7470070	0.85[EUR][1000 genomes]
rs7855143	0.85[EUR][1000 genomes]
rs7858000	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs916554	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916555	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs963115	0.88[EUR][1000 genomes]
rs969832	0.85[EUR][1000 genomes]
rs976499	0.86[EUR][1000 genomes]
rs9987486	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv1047164	chr9:118286742-118456851	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10124673	DEC1	cis	parietal	SCAN
rs10124673	HDHD3	cis	cerebellum	SCAN
rs10124673	C9orf29	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118277000-118292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:118283200-118291200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:118284400-118288000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:118285200-118289200	Enhancers	Fetal Lung	lung
5	chr9:118285400-118314600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:118286000-118288400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:118286400-118287200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:118286400-118288000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr9:118286400-118288400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:118286400-118288400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:118286400-118288400	Enhancers	Rectal Smooth Muscle	rectum
12	chr9:118286400-118289200	Enhancers	Colon Smooth Muscle	Colon
13	chr9:118286400-118289200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr9:118286600-118287000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr9:118286600-118287000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:118286600-118287000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:118286600-118287000	Enhancers	Adipose Nuclei	Adipose
18	chr9:118286600-118287000	Enhancers	Aorta	Aorta
19	chr9:118286600-118287000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:118286600-118287000	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr9:118286600-118287000	Flanking Active TSS	Osteobl	bone
22	chr9:118286600-118287200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:118286600-118287200	Enhancers	NHDF-Ad	bronchial
24	chr9:118286600-118287800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:118286600-118287800	Enhancers	NH-A	brain
26	chr9:118286600-118288400	Enhancers	Fetal Stomach	stomach
27	chr9:118286800-118287200	Flanking Active TSS	Fetal Kidney	kidney
28	chr9:118286800-118287200	Enhancers	HMEC	breast
29	chr9:118286800-118289600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:118286800-118293000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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