Variant report

Variant	rs6896228
Chromosome Location	chr5:177853532-177853533
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	chr5:177844389..177846173-chr5:177851202..177854065,2	MCF-7	breast:
2	chr5:177851551..177854301-chr5:177861521..177864094,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs12652099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546222	0.81[JPT][hapmap]
rs17052428	0.81[JPT][hapmap]
rs17081213	0.82[CHB][hapmap]
rs17081217	0.83[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs17081220	0.83[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs17081256	1.00[CEU][hapmap]
rs17081260	1.00[CEU][hapmap]
rs17081346	0.81[JPT][hapmap]
rs2546636	0.81[JPT][hapmap]
rs2647697	0.81[JPT][hapmap]
rs2672832	0.81[JPT][hapmap]
rs4618447	1.00[CEU][hapmap]
rs6601235	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs6868772	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886832	1.00[CEU][hapmap]
rs72648834	0.81[AMR][1000 genomes]
rs7706759	0.81[JPT][hapmap]
rs7726125	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs7728076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177840000-177855000	Weak transcription	Right Atrium	heart
2	chr5:177841200-177854400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:177846600-177856000	Weak transcription	Gastric	stomach
4	chr5:177847200-177854600	Weak transcription	Fetal Kidney	kidney
5	chr5:177848800-177859800	Strong transcription	Thymus	Thymus
6	chr5:177849200-177854400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:177849400-177854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:177849400-177855000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:177849600-177854400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:177849600-177855400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:177849600-177856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:177850400-177853800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:177850600-177855000	Weak transcription	Left Ventricle	heart
14	chr5:177850800-177855200	Weak transcription	Spleen	Spleen
15	chr5:177850800-177855600	Weak transcription	Fetal Heart	heart
16	chr5:177851400-177855600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:177851600-177853600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:177851600-177854400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:177851600-177855000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:177851800-177854200	Weak transcription	Fetal Lung	lung
21	chr5:177851800-177854400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:177851800-177854400	Weak transcription	Fetal Stomach	stomach
23	chr5:177852000-177854400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:177852000-177855000	Weak transcription	Placenta	Placenta
25	chr5:177852000-177855800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:177853000-177853600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:177853000-177857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:177853200-177858400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr5:177853400-177853600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr5:177853400-177854800	Weak transcription	Fetal Thymus	thymus
31	chr5:177853400-177856400	Enhancers	Fetal Brain Male	brain

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