Variant report

Variant	rs1016854
Chromosome Location	chr6:25277375-25277376
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	chr6:25272566..25274404-chr6:25275758..25278430,2	K562	blood:
2	chr6:25275009..25277575-chr6:25277975..25280731,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213972	Chromatin interaction
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1016855	0.91[CEU][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs2050044	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064211	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2078527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690067	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2744254	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2744267	0.85[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2744268	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914799	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs6926126	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs721036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723047	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748256	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9356971	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9356972	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366614	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379746	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379747	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379750	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9379751	0.83[YRI][hapmap]
rs9393636	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393637	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1016854	ZNF192	cis	parietal	SCAN
rs1016854	LENG9	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25271200-25277400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr6:25271200-25277400	Weak transcription	Fetal Thymus	thymus
3	chr6:25271200-25278400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:25275200-25277400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:25275600-25278400	Weak transcription	Pancreas	Pancrea
6	chr6:25275600-25278600	Weak transcription	Colonic Mucosa	Colon
7	chr6:25276000-25278200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:25276000-25278400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:25276200-25278200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:25276200-25278400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:25276200-25278600	Enhancers	Liver	Liver
12	chr6:25276200-25278600	Enhancers	Fetal Lung	lung
13	chr6:25276400-25278000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:25276400-25278000	Weak transcription	A549	lung
15	chr6:25276600-25277400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:25276600-25277400	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr6:25276600-25278200	Weak transcription	Stomach Mucosa	stomach
18	chr6:25276600-25278400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:25276800-25278400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:25277000-25277800	Enhancers	Brain Germinal Matrix	brain
21	chr6:25277000-25278400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:25277000-25278400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:25277000-25278600	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:25277200-25277400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:25277200-25277400	Enhancers	Stomach Smooth Muscle	stomach
26	chr6:25277200-25277600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:25277200-25277600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:25277200-25278400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:25277200-25278400	Enhancers	Fetal Intestine Small	intestine
30	chr6:25277200-25278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:25277200-25278600	Enhancers	Fetal Brain Male	brain
32	chr6:25277200-25278600	Enhancers	Fetal Intestine Large	intestine

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