Variant report

Variant	rs60885790
Chromosome Location	chr4:77043603-77043604
allele	A/C
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	POLR2A	chr4:77043419-77044705	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:77042420..77043971-chr4:77226885..77228605,2	K562	blood:
2	chr4:77037122..77039449-chr4:77042114..77044067,2	K562	blood:
3	chr4:77035266..77040414-chr4:77041570..77044067,5	K562	blood:
4	chr20:52812919..52815134-chr4:77041883..77044239,2	MCF-7	breast:

Variant related genes	Relation type
NUP54	TF binding region
ENSG00000118804	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs17001246	1.00[AMR][1000 genomes]
rs17001265	1.00[AMR][1000 genomes]
rs17001277	1.00[AMR][1000 genomes]
rs17001289	1.00[AMR][1000 genomes]
rs17001354	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17001355	1.00[AMR][1000 genomes]
rs17001359	1.00[AMR][1000 genomes]
rs17001362	1.00[AMR][1000 genomes]
rs17001366	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17001367	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17001596	1.00[AMR][1000 genomes]
rs17001619	1.00[AMR][1000 genomes]
rs17001626	1.00[AMR][1000 genomes]
rs17001627	1.00[AMR][1000 genomes]
rs17001636	1.00[AMR][1000 genomes]
rs17001639	1.00[AMR][1000 genomes]
rs41457447	1.00[AMR][1000 genomes]
rs4382064	1.00[AMR][1000 genomes]
rs4487370	1.00[AMR][1000 genomes]
rs55998455	1.00[AMR][1000 genomes]
rs56252973	1.00[AMR][1000 genomes]
rs56350100	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56653729	1.00[AMR][1000 genomes]
rs57005804	1.00[AMR][1000 genomes]
rs57415085	1.00[AMR][1000 genomes]
rs58605269	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60337837	1.00[AMR][1000 genomes]
rs60367545	1.00[AMR][1000 genomes]
rs61253655	1.00[AMR][1000 genomes]
rs61347786	1.00[AMR][1000 genomes]
rs61606865	1.00[AMR][1000 genomes]
rs62639704	1.00[AMR][1000 genomes]
rs73825715	1.00[AMR][1000 genomes]
rs73825720	1.00[AMR][1000 genomes]
rs73825882	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73826307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73826308	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73826312	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73826315	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73826333	1.00[AMR][1000 genomes]
rs73826378	1.00[AMR][1000 genomes]
rs73826380	1.00[AMR][1000 genomes]
rs73826385	1.00[AMR][1000 genomes]
rs73826388	1.00[AMR][1000 genomes]
rs7661525	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7685216	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers 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	18 gene(s)	inside rSNPs	diseases
4	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv275315	chr4:77040424-77056493	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1008318	chr4:77042356-77095658	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
9	nsv537144	chr4:77042356-77095658	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 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	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77032200-77049200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:77033000-77044800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:77033000-77046800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr4:77033000-77046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:77033000-77052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:77033200-77044400	Weak transcription	Spleen	Spleen
9	chr4:77033200-77045200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:77033200-77045600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr4:77033200-77046200	Strong transcription	Liver	Liver
12	chr4:77033200-77046600	Strong transcription	Fetal Lung	lung
13	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
16	chr4:77033400-77045600	Strong transcription	Adipose Nuclei	Adipose
17	chr4:77033400-77046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:77033400-77046000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:77033400-77046200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:77033400-77046400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:77033400-77046600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:77033400-77047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:77033400-77048200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:77033400-77052000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:77033400-77052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:77033600-77047600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:77034000-77045600	Strong transcription	Fetal Intestine Large	intestine
33	chr4:77034000-77046200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:77034000-77054000	Strong transcription	Dnd41	blood
35	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:77034200-77045400	Strong transcription	Placenta	Placenta
37	chr4:77034200-77045600	Strong transcription	Fetal Thymus	thymus
38	chr4:77034200-77046600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:77034400-77045600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:77034400-77046000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:77034400-77067200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:77035000-77068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:77035200-77062000	Weak transcription	Esophagus	oesophagus
44	chr4:77035200-77068600	Weak transcription	Pancreas	Pancrea
45	chr4:77035400-77066000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr4:77035600-77068400	Weak transcription	Right Ventricle	heart
47	chr4:77036400-77054600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr4:77037200-77046600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:77037400-77044800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:77037400-77045800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links