Variant report

Variant	rs16854895
Chromosome Location	chr1:179853418-179853419
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:179850203-179853448	K562	blood:	n/a	chr1:179852958-179852967 chr1:179853052-179853060 chr1:179852986-179852994 chr1:179852982-179852993
2	CHD1	chr1:179850810-179853436	IMR90	lung:	n/a	n/a
3	KAP1	chr1:179853232-179853434	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:
2	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:

Variant related genes	Relation type
ENSG00000272906	TF binding region
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10436866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12239940	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374504	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854828	0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854841	1.00[AMR][1000 genomes]
rs16854843	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854853	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854861	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854908	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854921	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854935	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854952	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs56725488	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59284984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59961638	0.89[AFR][1000 genomes];1.00[AMR][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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv518936	chr1:179847402-179858333	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179850200-179853600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:179850200-179853600	Active TSS	HMEC	breast
3	chr1:179850400-179853600	Active TSS	Aorta	Aorta
4	chr1:179850400-179853800	Active TSS	NHLF	lung
5	chr1:179850600-179853600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:179850600-179853600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:179850600-179853600	Active TSS	Colon Smooth Muscle	Colon
8	chr1:179850600-179853800	Active TSS	Fetal Intestine Large	intestine
9	chr1:179850800-179853600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:179850800-179853600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:179850800-179854200	Active TSS	GM12878-XiMat	blood
12	chr1:179852400-179853600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:179852400-179853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:179852600-179853600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:179852600-179853600	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr1:179852600-179854000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:179852800-179853600	Flanking Active TSS	Dnd41	blood
18	chr1:179852800-179854200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:179852800-179854400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:179852800-179858800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:179852800-179859800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:179852800-179860800	Weak transcription	Stomach Mucosa	stomach
23	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
24	chr1:179853000-179853600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:179853000-179853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:179853000-179853600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:179853000-179853600	Flanking Active TSS	A549	lung
28	chr1:179853000-179853800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr1:179853000-179853800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:179853000-179853800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:179853000-179853800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
32	chr1:179853000-179853800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:179853000-179854000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr1:179853000-179854000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:179853000-179854000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:179853000-179855400	Weak transcription	Ovary	ovary
37	chr1:179853000-179857000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:179853000-179858800	Weak transcription	Lung	lung
39	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
40	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:179853200-179853600	Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:179853200-179853600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:179853200-179853600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:179853200-179853600	Enhancers	Brain Cingulate Gyrus	brain
45	chr1:179853200-179853600	Weak transcription	Placenta	Placenta
46	chr1:179853200-179853600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:179853200-179853800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr1:179853200-179853800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:179853200-179853800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr1:179853200-179853800	Enhancers	Liver	Liver

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