Variant report

Variant	rs1555214
Chromosome Location	chr6:45928400-45928401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45919715..45922197-chr6:45926352..45928552,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3777580	0.95[LWK][hapmap];0.84[AFR][1000 genomes]
rs3777588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4714891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4714896	0.92[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1555214	OPN5	cis	parietal	SCAN
rs1555214	C6orf154	cis	cerebellum	SCAN
rs1555214	CRIP3	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45912800-45928400	Weak transcription	Spleen	Spleen
2	chr6:45918800-45938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:45920000-45934800	Weak transcription	Colonic Mucosa	Colon
4	chr6:45923200-45929200	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:45923200-45931200	Weak transcription	Fetal Intestine Large	intestine
6	chr6:45924400-45931000	Weak transcription	Fetal Intestine Small	intestine
7	chr6:45924600-45932400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:45924600-45934400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:45926400-45928600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:45926800-45928600	Enhancers	HSMM	muscle
11	chr6:45926800-45935000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:45927200-45928600	Enhancers	Fetal Muscle Leg	muscle
13	chr6:45927200-45929600	Enhancers	Placenta	Placenta
14	chr6:45927600-45928600	Enhancers	Fetal Lung	lung
15	chr6:45927800-45930600	Enhancers	Fetal Heart	heart
16	chr6:45927800-45932800	Weak transcription	NH-A	brain
17	chr6:45927800-45933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:45928000-45929000	Enhancers	Adipose Nuclei	Adipose
19	chr6:45928000-45933000	Weak transcription	HMEC	breast
20	chr6:45928200-45928400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:45928200-45928400	Bivalent Enhancer	Fetal Stomach	stomach
22	chr6:45928200-45928600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:45928200-45928600	Enhancers	Fetal Muscle Trunk	muscle
24	chr6:45928200-45928600	Enhancers	Left Ventricle	heart
25	chr6:45928200-45928600	Enhancers	Lung	lung
26	chr6:45928200-45928600	Enhancers	Right Atrium	heart
27	chr6:45928200-45928600	Enhancers	Right Ventricle	heart
28	chr6:45928200-45928600	Enhancers	Small Intestine	intestine
29	chr6:45928200-45928800	Enhancers	Psoas Muscle	Psoas
30	chr6:45928200-45936400	Weak transcription	Fetal Kidney	kidney
31	chr6:45928400-45928600	Enhancers	Spleen	Spleen
32	chr6:45928400-45929600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:45928400-45934200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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