Variant report

Variant	rs1828629
Chromosome Location	chr4:76600737-76600738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76600444..76602988-chr4:76649090..76651624,2	MCF-7	breast:
2	chr4:76596286..76601002-chr4:76645864..76652581,23	K562	blood:

Variant related genes	Relation type
ENSG00000138768	Chromatin interaction
ENSG00000138757	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10025315	0.82[EUR][1000 genomes]
rs11097069	0.81[EUR][1000 genomes]
rs11097070	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11736474	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13116639	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13118426	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13133699	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13137468	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13138717	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1464070	0.90[AMR][1000 genomes]
rs1464071	0.90[AMR][1000 genomes]
rs1546539	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1548175	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1553984	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1553986	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967495	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967496	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3796473	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3796485	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3796488	0.88[AMR][1000 genomes]
rs3853183	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4349625	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859403	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859542	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859543	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859544	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4859545	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859546	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859547	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859548	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531778	0.88[AMR][1000 genomes]
rs6531841	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531866	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531867	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6531868	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6826858	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6827809	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6832912	0.88[AMR][1000 genomes]
rs6835702	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6858741	0.95[AMR][1000 genomes]
rs7659408	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7672378	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674328	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7685459	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7691765	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9942164	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS 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	26 gene(s)	inside rSNPs	diseases
2	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
5	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599000-76619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:76599000-76620400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:76599200-76602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:76599200-76620000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:76599200-76640000	Weak transcription	Aorta	Aorta
6	chr4:76599400-76600800	Enhancers	Fetal Intestine Large	intestine
7	chr4:76599400-76600800	Enhancers	Fetal Intestine Small	intestine
8	chr4:76599400-76601400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:76599400-76603000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:76599400-76613000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:76599400-76617400	Weak transcription	Fetal Stomach	stomach
12	chr4:76599400-76619200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:76599400-76620400	Weak transcription	Left Ventricle	heart
14	chr4:76599600-76605200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:76599600-76607800	Weak transcription	Fetal Thymus	thymus
16	chr4:76599600-76608200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:76599600-76608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:76599600-76610800	Weak transcription	Brain Anterior Caudate	brain
19	chr4:76599600-76611200	Weak transcription	HSMMtube	muscle
20	chr4:76599600-76611400	Weak transcription	HSMM	muscle
21	chr4:76599600-76612200	Weak transcription	Brain Germinal Matrix	brain
22	chr4:76599600-76615600	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:76599600-76621600	Weak transcription	Fetal Lung	lung
24	chr4:76599600-76623400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:76599600-76624000	Weak transcription	Brain Substantia Nigra	brain
26	chr4:76599600-76639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:76599600-76639800	Weak transcription	Brain Angular Gyrus	brain
28	chr4:76599600-76639800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
30	chr4:76599800-76604400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:76599800-76604600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:76599800-76605000	Weak transcription	Primary T cells from cord blood	blood
33	chr4:76599800-76605200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:76599800-76605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:76599800-76608200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:76599800-76610800	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:76599800-76611800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:76599800-76612200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:76599800-76612600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:76599800-76612600	Weak transcription	A549	lung
41	chr4:76599800-76613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:76599800-76613600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:76599800-76619800	Weak transcription	Liver	Liver
44	chr4:76599800-76621200	Weak transcription	HepG2	liver
45	chr4:76599800-76627800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr4:76600400-76603000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:76600400-76603400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:76600400-76640000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:76600600-76600800	Enhancers	NHEK	skin
50	chr4:76600600-76603200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links