Variant report

Variant	rs2602454
Chromosome Location	chr16:81075289-81075290
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:
2	chr16:81073990..81076535-chr16:81110612..81112776,2	MCF-7	breast:
3	chr16:81074762..81077123-chr16:81078708..81080321,2	K562	blood:
4	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:
5	chr16:81075103..81077247-chr16:81078361..81079890,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000260213	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1563076	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2549889	0.83[AFR][1000 genomes]
rs2549890	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2549894	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs2602432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2602451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2911157	0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889232	1.00[AMR][1000 genomes]
rs5023851	1.00[AMR][1000 genomes]
rs6420420	1.00[AMR][1000 genomes]
rs7187102	1.00[AMR][1000 genomes]
rs7196170	1.00[AMR][1000 genomes]
rs804888	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs804898	1.00[AMR][1000 genomes]
rs804901	1.00[AMR][1000 genomes]
rs8049509	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs8177931	1.00[AMR][1000 genomes]
rs935945	0.87[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
7	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv995083	chr16:81050917-81076406	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81070600-81075800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:81071000-81075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:81071000-81075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:81071000-81075800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr16:81071000-81076400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr16:81071200-81075400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:81071200-81080400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:81071200-81080400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr16:81071200-81080600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr16:81071200-81082000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr16:81071200-81082400	Weak transcription	Stomach Mucosa	stomach
14	chr16:81071400-81079400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:81071400-81079600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr16:81071400-81079800	Strong transcription	Fetal Intestine Large	intestine
17	chr16:81071600-81080600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:81071800-81081800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr16:81072000-81079400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr16:81072200-81079400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr16:81072400-81079800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr16:81072600-81075800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr16:81072800-81075400	Weak transcription	NHEK	skin
24	chr16:81072800-81077800	Strong transcription	Hela-S3	cervix
25	chr16:81072800-81079000	Strong transcription	K562	blood
26	chr16:81073000-81079800	Strong transcription	Fetal Muscle Leg	muscle
27	chr16:81073200-81075800	Strong transcription	HepG2	liver
28	chr16:81073400-81075600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:81073600-81079800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr16:81073800-81075400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr16:81073800-81078000	Strong transcription	Small Intestine	intestine
32	chr16:81073800-81079400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr16:81073800-81079800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:81073800-81079800	Strong transcription	Fetal Thymus	thymus
35	chr16:81073800-81079800	Strong transcription	Dnd41	blood
36	chr16:81074000-81079200	Strong transcription	Fetal Brain Male	brain
37	chr16:81074000-81079400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr16:81074000-81079400	Strong transcription	Lung	lung
39	chr16:81074000-81079400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr16:81074000-81079800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr16:81074000-81079800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr16:81074000-81080000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr16:81074000-81080400	Strong transcription	Primary B cells from cord blood	blood
44	chr16:81074000-81080400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr16:81074000-81082400	Weak transcription	Fetal Heart	heart
46	chr16:81074200-81075600	Weak transcription	Brain Hippocampus Middle	brain
47	chr16:81074200-81079200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr16:81074200-81079400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr16:81074200-81079800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr16:81074400-81075400	Genic enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links