Variant report

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39194267..39198294-chr6:39269067..39272722,11	MCF-7	breast:
2	chr6:39195692..39197449-chr6:39269693..39272549,3	K562	blood:
3	chr6:39195179..39198442-chr6:39267374..39272549,7	K562	blood:
4	chr6:39153346..39156056-chr6:39270382..39273616,3	K562	blood:
5	chr6:39133945..39136207-chr6:39268865..39270685,2	K562	blood:
6	chr6:39163723..39165690-chr6:39268999..39271055,3	MCF-7	breast:
7	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
8	chr6:39133828..39135626-chr6:39269069..39271952,36	K562	blood:
9	chr6:39146215..39148913-chr6:39269564..39272045,2	MCF-7	breast:
10	chr6:39239173..39241787-chr6:39269864..39271484,2	MCF-7	breast:
11	chr6:39133802..39135109-chr6:39270035..39271889,35	MCF-7	breast:
12	chr6:39267482..39269226-chr6:39269492..39271428,2	MCF-7	breast:
13	chr6:39131553..39138589-chr6:39265255..39275264,18	MCF-7	breast:
14	chr6:39235849..39239507-chr6:39267408..39272188,7	MCF-7	breast:
15	chr6:39265273..39267216-chr6:39269538..39271599,2	MCF-7	breast:
16	chr6:39235093..39238743-chr6:39267391..39271695,7	MCF-7	breast:
17	chr6:39154173..39155788-chr6:39270095..39272270,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1078911	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807204	0.84[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10807205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12194951	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs2758862	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs34102522	0.93[EUR][1000 genomes]
rs6940480	0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs72855524	0.94[EUR][1000 genomes]
rs9349112	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9349113	0.80[ASN][1000 genomes]
rs9369111	0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9380846	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9394581	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs9394583	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9471058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv533806	chr6:39270073-39397337	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2395721	CPNE5	cis	parietal	SCAN
rs2395721	KCNK17	cis	parietal	SCAN
rs2395721	TBCC	cis	cerebellum	SCAN
rs2395721	RPL10A	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39262600-39270600	Weak transcription	Colonic Mucosa	Colon
2	chr6:39265400-39270800	Weak transcription	Fetal Lung	lung
3	chr6:39265400-39270800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:39265600-39280800	Weak transcription	Right Atrium	heart
5	chr6:39266200-39270800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:39266600-39270600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:39266600-39270600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:39269000-39271200	Enhancers	Placenta	Placenta
9	chr6:39269400-39271200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:39270000-39270600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:39270200-39271000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:39270200-39271200	Enhancers	Liver	Liver
13	chr6:39270200-39271600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:39270400-39270600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:39270400-39270800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr6:39270400-39270800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr6:39270400-39271000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:39270400-39271000	Enhancers	Fetal Thymus	thymus
19	chr6:39270400-39271400	Enhancers	Fetal Intestine Small	intestine
20	chr6:39270400-39272800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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