Variant report

Variant	rs16890722
Chromosome Location	chr5:61689743-61689744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:61689536-61689887	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:61680148-61692922	K562	blood:	n/a	n/a
3	POLR2A	chr5:61689634-61690874	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:61689283-61690152	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:61688987..61691804-chr5:61707990..61709990,3	K562	blood:
2	chr5:61684151..61688740-chr5:61689725..61696494,7	K562	blood:
3	chr5:61687760..61696371-chr5:61696777..61701236,17	K562	blood:
4	chr5:61675578..61677297-chr5:61689540..61692147,2	K562	blood:
5	chr5:61682102..61684562-chr5:61689312..61693081,3	K562	blood:
6	chr5:61687643..61690637-chr5:61717431..61720022,2	K562	blood:
7	chr5:61683430..61685907-chr5:61688335..61689954,2	MCF-7	breast:

No data

Variant related genes	Relation type
DIMT1	TF binding region
ENSG00000086189	Chromatin interaction
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs16890603	1.00[AMR][1000 genomes]
rs16890718	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16890748	1.00[AMR][1000 genomes]
rs16890754	1.00[AMR][1000 genomes]
rs16890773	1.00[AMR][1000 genomes]
rs16890775	1.00[AMR][1000 genomes]
rs16890823	1.00[AMR][1000 genomes]
rs17349793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2053695	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58504293	1.00[AMR][1000 genomes]
rs60001470	1.00[AMR][1000 genomes]
rs60115750	1.00[AMR][1000 genomes]
rs61118775	1.00[AMR][1000 genomes]
rs6864377	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6868330	1.00[AMR][1000 genomes]
rs6873199	1.00[AMR][1000 genomes]
rs6875068	1.00[AMR][1000 genomes]
rs6877630	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6883414	1.00[AMR][1000 genomes]
rs6886500	1.00[AMR][1000 genomes]
rs6886876	1.00[AMR][1000 genomes]
rs6887244	1.00[AMR][1000 genomes]
rs6893193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73102077	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73104048	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73105912	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73105928	1.00[AMR][1000 genomes]
rs73105939	1.00[AMR][1000 genomes]
rs73105968	1.00[AMR][1000 genomes]
rs73105990	1.00[AMR][1000 genomes]
rs73105993	1.00[AMR][1000 genomes]
rs73106001	1.00[AMR][1000 genomes]
rs73108048	1.00[AMR][1000 genomes]
rs73108058	1.00[AMR][1000 genomes]
rs73108070	1.00[AMR][1000 genomes]
rs73108074	1.00[AMR][1000 genomes]
rs73108089	1.00[AMR][1000 genomes]
rs73108092	1.00[AMR][1000 genomes]
rs73110006	1.00[AMR][1000 genomes]
rs73117401	1.00[AMR][1000 genomes]
rs73119503	1.00[AMR][1000 genomes]
rs73119521	1.00[AMR][1000 genomes]
rs73119543	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7711860	1.00[AMR][1000 genomes]
rs7725660	1.00[AMR][1000 genomes]
rs7728166	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7729131	1.00[AMR][1000 genomes]
rs7735150	1.00[AFR][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	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:61642600-61699200	Weak transcription	Gastric	stomach
4	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:61647000-61690000	Weak transcription	Spleen	Spleen
6	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:61658400-61691800	Strong transcription	Dnd41	blood
9	chr5:61659800-61695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
14	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:61667000-61691200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr5:61667000-61691600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:61667000-61697200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:61667400-61697200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:61667600-61697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:61668600-61697000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:61669200-61690200	Strong transcription	HUVEC	blood vessel
24	chr5:61669400-61690800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:61670000-61697200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:61670800-61690000	Weak transcription	Aorta	Aorta
27	chr5:61672000-61698600	Weak transcription	Stomach Mucosa	stomach
28	chr5:61675000-61697800	Weak transcription	Small Intestine	intestine
29	chr5:61676800-61697800	Weak transcription	Right Atrium	heart
30	chr5:61676800-61699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:61679200-61691000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:61679400-61690000	Weak transcription	Lung	lung
33	chr5:61679400-61692200	Strong transcription	Fetal Thymus	thymus
34	chr5:61679600-61691200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr5:61679600-61697000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:61679600-61697600	Strong transcription	Liver	Liver
37	chr5:61680000-61696000	Strong transcription	HSMM	muscle
38	chr5:61680000-61697200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:61680000-61697200	Strong transcription	Adipose Nuclei	Adipose
40	chr5:61680200-61691200	Strong transcription	Osteobl	bone
41	chr5:61680200-61694800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:61680200-61696000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:61680200-61697000	Strong transcription	Primary T cells from cord blood	blood
44	chr5:61680200-61697000	Strong transcription	Fetal Intestine Large	intestine
45	chr5:61680400-61697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:61680800-61690800	Strong transcription	Primary B cells from cord blood	blood
47	chr5:61681000-61691200	Strong transcription	A549	lung
48	chr5:61681400-61690000	Weak transcription	Fetal Intestine Small	intestine
49	chr5:61681400-61690800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr5:61681600-61690200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links