Variant report

Variant	rs6877016
Chromosome Location	chr5:177855357-177855358
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	chr5:177851066..177853109-chr5:177854719..177857640,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10062593	1.00[CEU][hapmap]
rs11956401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17052428	1.00[CEU][hapmap]
rs17081203	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17081205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17081346	1.00[CEU][hapmap]
rs2173435	1.00[EUR][1000 genomes]
rs2546634	1.00[CEU][hapmap]
rs533024	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs535011	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs549216	1.00[EUR][1000 genomes]
rs572273	1.00[EUR][1000 genomes]
rs621117	1.00[EUR][1000 genomes]
rs681420	1.00[EUR][1000 genomes]
rs6868472	1.00[CEU][hapmap]
rs6868772	1.00[CEU][hapmap]
rs6868991	1.00[CEU][hapmap]
rs7726676	1.00[EUR][1000 genomes]
rs869405	1.00[CEU][hapmap]

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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177846600-177856000	Weak transcription	Gastric	stomach
2	chr5:177848800-177859800	Strong transcription	Thymus	Thymus
3	chr5:177849600-177855400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:177849600-177856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:177850800-177855600	Weak transcription	Fetal Heart	heart
6	chr5:177851400-177855600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:177852000-177855800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:177853000-177857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:177853200-177858400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:177853400-177856400	Enhancers	Fetal Brain Male	brain
11	chr5:177853600-177855400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:177853600-177856600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:177854200-177856400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:177854200-177857600	Enhancers	Fetal Lung	lung
15	chr5:177854400-177855800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr5:177854400-177856400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:177854400-177856400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:177854400-177856600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:177854400-177856600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:177854400-177856800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:177854400-177856800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:177854400-177857200	Enhancers	Fetal Stomach	stomach
23	chr5:177854400-177857400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:177854800-177856200	Strong transcription	Fetal Thymus	thymus
25	chr5:177854800-177856600	Enhancers	Brain Cingulate Gyrus	brain
26	chr5:177855000-177855600	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr5:177855000-177856000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:177855000-177856000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr5:177855000-177856200	Enhancers	Brain Angular Gyrus	brain
30	chr5:177855000-177856400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:177855000-177856400	Weak transcription	Fetal Kidney	kidney
32	chr5:177855000-177856600	Enhancers	Brain Germinal Matrix	brain
33	chr5:177855000-177856800	Enhancers	Brain Anterior Caudate	brain
34	chr5:177855000-177856800	Enhancers	Brain Hippocampus Middle	brain
35	chr5:177855000-177856800	Enhancers	Left Ventricle	heart
36	chr5:177855000-177857000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr5:177855000-177857000	Enhancers	Psoas Muscle	Psoas
38	chr5:177855000-177857200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr5:177855000-177857200	Enhancers	Placenta	Placenta
40	chr5:177855000-177857200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:177855200-177855600	Weak transcription	Fetal Brain Female	brain
42	chr5:177855200-177855600	Weak transcription	Right Atrium	heart
43	chr5:177855200-177855800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:177855200-177856600	Enhancers	Brain Substantia Nigra	brain
45	chr5:177855200-177856800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr5:177855200-177856800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:177855200-177857000	Enhancers	Spleen	Spleen
48	chr5:177855200-177857200	Enhancers	Liver	Liver
49	chr5:177855200-177857200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr5:177855200-177857200	Enhancers	Lung	lung

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