Variant report

Variant	rs6458479
Chromosome Location	chr6:45955173-45955174
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	chr6:45942534..45945438-chr6:45953727..45956305,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1338470	0.95[ASN][1000 genomes]
rs1338471	1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1361216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs1416170	1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1535108	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2022419	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs2894658	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3777606	0.80[MEX][hapmap]
rs3777612	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs4711840	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs4714900	0.85[ASN][1000 genomes]
rs6458480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458481	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458482	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458483	0.87[ASN][1000 genomes]
rs6921959	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930840	0.84[MEX][hapmap]
rs7772905	0.83[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs7773297	0.83[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs9395142	0.86[ASN][1000 genomes]
rs9472632	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9472651	0.87[ASN][1000 genomes]
rs9472653	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.86[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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025846	chr6:45955173-46047269	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6458479	CLIC5	cis	parietal	SCAN
rs6458479	CLIC5	cis	Thyroid	GTEx
rs6458479	TNFRSF21	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45950600-45960200	Enhancers	Psoas Muscle	Psoas
2	chr6:45951000-45955200	Enhancers	Right Atrium	heart
3	chr6:45951400-45956400	Weak transcription	Small Intestine	intestine
4	chr6:45952400-45961400	Enhancers	Fetal Heart	heart
5	chr6:45952800-45956800	Enhancers	Fetal Muscle Leg	muscle
6	chr6:45953400-45956400	Weak transcription	Lung	lung
7	chr6:45953400-45965600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:45953800-45957000	Enhancers	Fetal Intestine Large	intestine
9	chr6:45954000-45956600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:45954200-45956800	Enhancers	Fetal Intestine Small	intestine
11	chr6:45954200-45956800	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr6:45954200-45957000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:45954600-45955400	Enhancers	Fetal Kidney	kidney
14	chr6:45954600-45955400	Enhancers	HSMMtube	muscle
15	chr6:45954600-45955600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr6:45954600-45956000	Weak transcription	Left Ventricle	heart
17	chr6:45954600-45956200	Enhancers	Stomach Mucosa	stomach
18	chr6:45954800-45955400	Enhancers	Colonic Mucosa	Colon
19	chr6:45954800-45955800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr6:45954800-45956800	Enhancers	Duodenum Mucosa	Duodenum
21	chr6:45954800-45960200	Weak transcription	Gastric	stomach
22	chr6:45955000-45960800	Enhancers	Right Ventricle	heart

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