Variant report

Variant	rs6601073
Chromosome Location	chr5:179177271-179177272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179158059..179161360-chr5:179174107..179178623,5	MCF-7	breast:
2	chr5:179166206..179168517-chr5:179176476..179179040,2	MCF-7	breast:
3	chr5:179124686..179128600-chr5:179174802..179178197,3	MCF-7	breast:
4	chr5:179175737..179178528-chr5:179180784..179182506,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127022	Chromatin interaction
ENSG00000161021	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1019443	0.89[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10447303	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10447304	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10794700	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10903245	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11744662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12374446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12374485	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12522926	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12652934	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs13172893	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13174472	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13182141	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs13184690	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34329357	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34646062	0.85[CEU][hapmap]
rs34785307	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35320050	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3797774	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56227602	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56807514	0.89[EUR][1000 genomes]
rs62404348	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62406180	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7736300	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6601073	CANX	cis	parietal	SCAN
rs6601073	C5orf45	cis	cerebellum	SCAN
rs6601073	CANX	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179161000-179181200	Weak transcription	Aorta	Aorta
2	chr5:179161000-179181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:179161000-179181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:179161800-179177400	Weak transcription	Fetal Kidney	kidney
5	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
6	chr5:179162000-179181200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:179162000-179181400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:179162000-179181800	Weak transcription	NHLF	lung
9	chr5:179162000-179186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:179162000-179186000	Weak transcription	HSMM	muscle
11	chr5:179162000-179186200	Weak transcription	HMEC	breast
12	chr5:179162000-179186600	Weak transcription	Hela-S3	cervix
13	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:179162600-179189000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:179163200-179181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:179163800-179180000	Weak transcription	Fetal Brain Male	brain
17	chr5:179164400-179179000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:179164400-179181600	Weak transcription	HUVEC	blood vessel
19	chr5:179164600-179186600	Weak transcription	NH-A	brain
20	chr5:179165000-179181200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:179165400-179184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:179165600-179181800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:179165800-179188800	Weak transcription	Brain Germinal Matrix	brain
24	chr5:179166200-179181200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:179166400-179181400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:179166400-179181400	Weak transcription	Fetal Intestine Large	intestine
27	chr5:179167000-179186600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:179167200-179181000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:179167200-179188800	Weak transcription	NHEK	skin
30	chr5:179167400-179181600	Weak transcription	Fetal Lung	lung
31	chr5:179167800-179181000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:179168000-179185800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:179168400-179181200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:179168600-179181000	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:179168600-179181000	Weak transcription	Psoas Muscle	Psoas
36	chr5:179171800-179181000	Weak transcription	Ovary	ovary
37	chr5:179171800-179188800	Weak transcription	Colonic Mucosa	Colon
38	chr5:179173400-179178400	Strong transcription	Fetal Stomach	stomach
39	chr5:179174400-179177400	Weak transcription	Right Ventricle	heart
40	chr5:179174400-179177800	Strong transcription	Fetal Muscle Leg	muscle
41	chr5:179174400-179180800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:179174400-179181000	Weak transcription	A549	lung
43	chr5:179174400-179181200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:179174400-179181200	Weak transcription	Primary B cells from cord blood	blood
45	chr5:179174400-179181400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:179174400-179181400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:179174400-179182000	Weak transcription	Brain Anterior Caudate	brain
48	chr5:179174400-179186600	Weak transcription	Esophagus	oesophagus
49	chr5:179174400-179192200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:179174600-179177600	Weak transcription	Left Ventricle	heart

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