Variant report

Variant	rs214054
Chromosome Location	chr6:25559898-25559899
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	chr6:25553463..25555118-chr6:25558939..25560459,2	MCF-7	breast:
2	chr6:25558691..25560985-chr6:26021184..26023222,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196176	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs118855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1206523	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12526480	0.83[GIH][hapmap]
rs212934	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs214048	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs214053	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs214056	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs214057	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs214058	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs214059	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs214060	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs214065	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs368638	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804123	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs394201	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs431659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441460	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452447	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs454095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530145	0.88[ASN][1000 genomes]
rs6913974	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9379771	0.95[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv970674	chr6:25559891-25564508	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs214054	HIST1H2BE	cis	parietal	SCAN
rs214054	SLC17A1	cis	cerebellum	SCAN
rs214054	PRSS16	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25471600-25597200	Weak transcription	Gastric	stomach
2	chr6:25516800-25606400	Weak transcription	Lung	lung
3	chr6:25522400-25588600	Weak transcription	HMEC	breast
4	chr6:25523000-25577200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:25530800-25584200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:25538600-25563600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:25538600-25592800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:25539000-25561200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:25539200-25582000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:25539600-25565200	Weak transcription	Aorta	Aorta
11	chr6:25540600-25580200	Weak transcription	Fetal Thymus	thymus
12	chr6:25541400-25576200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:25541600-25584400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:25542400-25563600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:25543800-25562000	Weak transcription	Adipose Nuclei	Adipose
17	chr6:25544000-25593600	Weak transcription	Fetal Lung	lung
18	chr6:25544600-25565000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:25547200-25600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:25551400-25565400	Weak transcription	Fetal Intestine Large	intestine
21	chr6:25553800-25565200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:25554200-25563800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:25554400-25567600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
25	chr6:25557200-25560200	Weak transcription	Pancreas	Pancrea
26	chr6:25557200-25591400	Weak transcription	Ovary	ovary
27	chr6:25559200-25560000	Strong transcription	Primary T cells from cord blood	blood
28	chr6:25559600-25560000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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