Variant report

Variant	rs13135639
Chromosome Location	chr4:77056808-77056809
allele	A/G
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	chr4:77056429-77057181	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:77055702..77058489-chr4:77060298..77061923,3	K562	blood:
2	chr4:77056276..77058049-chr4:77058093..77060100,3	K562	blood:
3	chr4:77056272..77058794-chr4:77068022..77070741,2	MCF-7	breast:

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11734758	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941852	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11946345	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108645	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13110133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126384	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241588	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241589	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241590	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4288034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337755	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498155	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544733	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4552490	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4730	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859616	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532203	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532204	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532208	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532244	0.80[AMR][1000 genomes]
rs6829581	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657598	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675253	0.83[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	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
8	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
9	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
10	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
6	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:77034400-77067200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:77035000-77068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:77035200-77062000	Weak transcription	Esophagus	oesophagus
15	chr4:77035200-77068600	Weak transcription	Pancreas	Pancrea
16	chr4:77035400-77066000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:77035600-77068400	Weak transcription	Right Ventricle	heart
18	chr4:77038200-77062000	Weak transcription	Aorta	Aorta
19	chr4:77039000-77061800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:77039000-77068200	Weak transcription	Psoas Muscle	Psoas
21	chr4:77039000-77068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:77039600-77057400	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:77040800-77063200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:77041800-77057600	Weak transcription	Ovary	ovary
25	chr4:77043600-77059400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:77043800-77059800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:77044200-77068200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:77044400-77058400	Weak transcription	Brain Angular Gyrus	brain
29	chr4:77044400-77059200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:77044400-77059600	Weak transcription	HSMMtube	muscle
31	chr4:77044400-77062000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:77044600-77061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:77044600-77062000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:77044800-77057600	Weak transcription	Lung	lung
35	chr4:77045000-77068600	Weak transcription	Spleen	Spleen
36	chr4:77047000-77063400	Strong transcription	Liver	Liver
37	chr4:77047200-77065600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:77048600-77065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:77048800-77058000	Strong transcription	HSMM	muscle
40	chr4:77048800-77065600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:77049200-77063400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr4:77049200-77064800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:77049200-77065600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:77049800-77057200	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:77050200-77061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:77050200-77068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr4:77050600-77057400	Weak transcription	Brain Germinal Matrix	brain
48	chr4:77050600-77062000	Weak transcription	Fetal Heart	heart
49	chr4:77050800-77059200	Weak transcription	A549	lung
50	chr4:77051000-77061000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links