Variant report

Variant	rs4288034
Chromosome Location	chr4:77068016-77068017
allele	C/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	STAT3	chr4:77068013-77068191	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:77067944-77068061	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:77050141..77053778-chr4:77066166..77070004,4	MCF-7	breast:
2	chr4:77066331..77070645-chr4:77133023..77136401,5	K562	blood:
3	chr4:77065569..77067596-chr4:77067716..77071190,4	MCF-7	breast:
4	chr4:77067778..77069460-chr4:77134577..77136401,2	K562	blood:
5	chr4:77054225..77056351-chr4:77067941..77069735,2	MCF-7	breast:

Variant related genes	Relation type
NUP54	TF binding region
ENSG00000138750	Chromatin interaction
ENSG00000189157	Chromatin interaction
ENSG00000138760	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11723400	0.80[CEU][hapmap]
rs11734758	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941852	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11946345	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108645	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13110133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126384	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151075	0.82[YRI][hapmap]
rs14773	0.86[YRI][hapmap]
rs4241588	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241589	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241590	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4337755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498155	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4538520	0.81[CEU][hapmap]
rs4544733	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4552490	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859616	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532204	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532208	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6532244	0.80[AMR][1000 genomes]
rs6829581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838435	0.81[YRI][hapmap]
rs6850228	0.86[YRI][hapmap]
rs735697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657598	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7657823	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
3	chr4:77035000-77068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:77035200-77068600	Weak transcription	Pancreas	Pancrea
5	chr4:77035600-77068400	Weak transcription	Right Ventricle	heart
6	chr4:77039000-77068200	Weak transcription	Psoas Muscle	Psoas
7	chr4:77039000-77068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:77044200-77068200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:77045000-77068600	Weak transcription	Spleen	Spleen
10	chr4:77051400-77068600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:77057000-77068200	Weak transcription	Colonic Mucosa	Colon
12	chr4:77058800-77068400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:77062400-77068600	Weak transcription	Aorta	Aorta
14	chr4:77062400-77068600	Weak transcription	Esophagus	oesophagus
15	chr4:77062400-77068600	Weak transcription	Lung	lung
16	chr4:77062600-77068400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:77062600-77068600	Weak transcription	Left Ventricle	heart
18	chr4:77062800-77068200	Weak transcription	Ovary	ovary
19	chr4:77063200-77068200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:77063400-77068200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:77063400-77068200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:77065200-77068600	Weak transcription	Placenta	Placenta
23	chr4:77065400-77068400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:77065600-77068200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:77065600-77068200	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:77065600-77068200	Weak transcription	Fetal Thymus	thymus
27	chr4:77065600-77068200	Weak transcription	Thymus	Thymus
28	chr4:77065600-77068400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:77065600-77068400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:77065600-77068400	Weak transcription	HSMMtube	muscle
31	chr4:77066000-77068200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:77066000-77068400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:77066000-77070800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr4:77066600-77068200	Enhancers	Liver	Liver
35	chr4:77066600-77068400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:77066600-77068400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr4:77066600-77070800	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr4:77066800-77068200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr4:77066800-77068200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:77066800-77068200	Enhancers	Adipose Nuclei	Adipose
41	chr4:77066800-77068200	Enhancers	Fetal Lung	lung
42	chr4:77066800-77068400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr4:77066800-77068400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:77067000-77068200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:77067000-77068400	Enhancers	Brain Cingulate Gyrus	brain
46	chr4:77067000-77069000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:77067000-77070600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr4:77067200-77068200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr4:77067200-77068400	Enhancers	Primary B cells from cord blood	blood
50	chr4:77067200-77068600	Enhancers	Stomach Mucosa	stomach

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