Variant report

Variant	rs62389411
Chromosome Location	chr5:177856061-177856062
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177851066..177853109-chr5:177854719..177857640,2	MCF-7	breast:
2	chr5:177855622..177857824-chr5:177858602..177861991,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10050728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063441	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063674	1.00[ASN][1000 genomes]
rs11956256	1.00[ASN][1000 genomes]
rs11956284	1.00[ASN][1000 genomes]
rs17081205	0.94[EUR][1000 genomes]
rs28657401	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673403	1.00[ASN][1000 genomes]
rs4357054	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4541676	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4976725	1.00[ASN][1000 genomes]
rs59697910	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60667997	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60745554	0.89[EUR][1000 genomes]
rs62389412	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62389413	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6422347	0.89[EUR][1000 genomes]
rs6601236	0.89[EUR][1000 genomes]
rs6601237	0.89[EUR][1000 genomes]
rs6882668	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177848800-177859800	Strong transcription	Thymus	Thymus
2	chr5:177853000-177857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:177853200-177858400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:177853400-177856400	Enhancers	Fetal Brain Male	brain
5	chr5:177853600-177856600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:177854200-177856400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:177854200-177857600	Enhancers	Fetal Lung	lung
8	chr5:177854400-177856400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:177854400-177856400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:177854400-177856600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:177854400-177856600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr5:177854400-177856800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:177854400-177856800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:177854400-177857200	Enhancers	Fetal Stomach	stomach
15	chr5:177854400-177857400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:177854800-177856200	Strong transcription	Fetal Thymus	thymus
17	chr5:177854800-177856600	Enhancers	Brain Cingulate Gyrus	brain
18	chr5:177855000-177856200	Enhancers	Brain Angular Gyrus	brain
19	chr5:177855000-177856400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:177855000-177856400	Weak transcription	Fetal Kidney	kidney
21	chr5:177855000-177856600	Enhancers	Brain Germinal Matrix	brain
22	chr5:177855000-177856800	Enhancers	Brain Anterior Caudate	brain
23	chr5:177855000-177856800	Enhancers	Brain Hippocampus Middle	brain
24	chr5:177855000-177856800	Enhancers	Left Ventricle	heart
25	chr5:177855000-177857000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr5:177855000-177857000	Enhancers	Psoas Muscle	Psoas
27	chr5:177855000-177857200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr5:177855000-177857200	Enhancers	Placenta	Placenta
29	chr5:177855000-177857200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:177855200-177856600	Enhancers	Brain Substantia Nigra	brain
31	chr5:177855200-177856800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr5:177855200-177856800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:177855200-177857000	Enhancers	Spleen	Spleen
34	chr5:177855200-177857200	Enhancers	Liver	Liver
35	chr5:177855200-177857200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr5:177855200-177857200	Enhancers	Lung	lung
37	chr5:177855400-177856200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr5:177855400-177856400	Enhancers	H1 Cell Line	embryonic stem cell
39	chr5:177855400-177856600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:177855400-177857200	Enhancers	Esophagus	oesophagus
41	chr5:177855600-177856200	Enhancers	Stomach Smooth Muscle	stomach
42	chr5:177855600-177856400	Enhancers	Fetal Muscle Leg	muscle
43	chr5:177855600-177856600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr5:177855600-177856800	Enhancers	Fetal Heart	heart
45	chr5:177855600-177856800	Enhancers	Right Atrium	heart
46	chr5:177855600-177858200	Enhancers	Pancreas	Pancrea
47	chr5:177855800-177856400	Enhancers	Fetal Intestine Small	intestine
48	chr5:177855800-177856400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr5:177855800-177857000	Enhancers	Right Ventricle	heart
50	chr5:177855800-177857600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links