Variant report

Variant	rs16854908
Chromosome Location	chr1:179857131-179857132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179857047..179859272-chr1:179914724..179916523,2	K562	blood:
2	chr1:179856867..179859704-chr1:179868315..179870029,2	K562	blood:
3	chr1:179856725..179858627-chr1:179861974..179863939,2	K562	blood:
4	chr1:179855626..179859704-chr1:179868315..179870321,3	K562	blood:
5	chr1:179849895..179854138-chr1:179857075..179860267,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000272906	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]
rs16854895	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]
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	chr1:179852800-179858800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179852800-179859800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179852800-179860800	Weak transcription	Stomach Mucosa	stomach
4	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
5	chr1:179853000-179858800	Weak transcription	Lung	lung
6	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
7	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:179853200-179858800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:179853200-179858800	Weak transcription	Left Ventricle	heart
10	chr1:179853200-179859800	Weak transcription	Colonic Mucosa	Colon
11	chr1:179853200-179859800	Weak transcription	Gastric	stomach
12	chr1:179853200-179859800	Weak transcription	Pancreas	Pancrea
13	chr1:179853200-179861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:179853400-179858800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:179853400-179859000	Weak transcription	HSMMtube	muscle
18	chr1:179853400-179859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
21	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
23	chr1:179853600-179858800	Weak transcription	Fetal Kidney	kidney
24	chr1:179853600-179859800	Weak transcription	Aorta	Aorta
25	chr1:179853600-179861600	Strong transcription	Placenta	Placenta
26	chr1:179853800-179857600	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr1:179853800-179858800	Weak transcription	Fetal Stomach	stomach
28	chr1:179853800-179859200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:179853800-179861200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:179853800-179863200	Strong transcription	Fetal Lung	lung
31	chr1:179854000-179857200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:179854000-179857600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:179854000-179857600	Strong transcription	HSMM	muscle
34	chr1:179854000-179857600	Strong transcription	HUVEC	blood vessel
35	chr1:179854000-179858400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:179854000-179858800	Weak transcription	Fetal Intestine Small	intestine
37	chr1:179854000-179859000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:179854000-179859800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:179854000-179865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
41	chr1:179854200-179859400	Weak transcription	HepG2	liver
42	chr1:179854200-179859800	Weak transcription	Thymus	Thymus
43	chr1:179854200-179863000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:179854200-179863000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:179854200-179866600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
47	chr1:179854400-179857400	Weak transcription	Fetal Brain Female	brain
48	chr1:179854400-179857400	Weak transcription	K562	blood
49	chr1:179854400-179857600	Genic enhancers	Dnd41	blood
50	chr1:179854600-179857200	Weak transcription	Brain Angular Gyrus	brain

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