Variant report

Variant	rs60618725
Chromosome Location	chr4:90041790-90041791
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	chr4:90031396..90034227-chr4:90041663..90045608,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-4	chr4:90041199-90042022	NONHSAT097383

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction
ENSG00000180346	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11097208	0.83[AMR][1000 genomes]
rs12640018	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13138280	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1398940	0.81[ASN][1000 genomes]
rs1398944	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015027	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015052	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1708668	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1708669	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1708670	0.84[ASN][1000 genomes]
rs1708681	0.85[ASN][1000 genomes]
rs1795722	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1795727	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1795729	0.82[ASN][1000 genomes]
rs1795734	0.81[ASN][1000 genomes]
rs1795738	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1849597	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1921684	0.83[AMR][1000 genomes]
rs1961979	0.83[AMR][1000 genomes]
rs2018779	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2090031	0.91[ASN][1000 genomes]
rs2464514	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2670623	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2704571	0.85[ASN][1000 genomes]
rs28600923	0.86[ASN][1000 genomes]
rs28628620	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869971	0.83[AMR][1000 genomes]
rs2869972	0.83[AMR][1000 genomes]
rs28712360	0.83[AMR][1000 genomes]
rs2904261	0.83[AMR][1000 genomes]
rs34845187	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35624987	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4285052	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4450885	0.83[AMR][1000 genomes]
rs4642211	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59924504	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62306363	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62306364	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62306390	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62306391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62306397	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6821678	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6852373	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6853480	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72877642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656238	0.83[AMR][1000 genomes]
rs7658455	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7659904	0.83[AMR][1000 genomes]
rs7660314	0.83[AMR][1000 genomes]
rs7680864	0.83[AMR][1000 genomes]
rs7692291	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9307061	0.83[AMR][1000 genomes]
rs9991237	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
5	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
6	chr4:90033600-90049200	Weak transcription	Gastric	stomach
7	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
8	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:90034000-90042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
14	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
18	chr4:90035200-90042600	Weak transcription	K562	blood
19	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:90035600-90041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:90035600-90043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood
25	chr4:90039200-90042800	Weak transcription	HepG2	liver
26	chr4:90039200-90044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:90039800-90043400	Weak transcription	Placenta	Placenta
28	chr4:90039800-90043800	Weak transcription	Liver	Liver
29	chr4:90040600-90042800	Enhancers	A549	lung
30	chr4:90041000-90043200	Weak transcription	HMEC	breast
31	chr4:90041200-90042600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:90041200-90043200	Weak transcription	NHEK	skin
33	chr4:90041400-90043800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:90041600-90041800	Enhancers	Fetal Intestine Large	intestine
35	chr4:90041600-90043000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:90041600-90044000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:90041600-90044000	Weak transcription	NH-A	brain
38	chr4:90041600-90045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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