Variant report

Variant	rs6601235
Chromosome Location	chr5:177857349-177857350
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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10059706	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12652099	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs17081256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17081260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4618447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60745554	0.97[ASN][1000 genomes]
rs61636631	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6422347	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6422348	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6601236	0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6601237	0.95[ASN][1000 genomes]
rs6868772	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs6882668	0.95[ASN][1000 genomes]
rs6886832	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6892799	0.95[ASN][1000 genomes]
rs6896228	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs72648835	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72648836	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7726125	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7728076	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177848800-177859800	Strong transcription	Thymus	Thymus
2	chr5:177853200-177858400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:177854200-177857600	Enhancers	Fetal Lung	lung
4	chr5:177854400-177857400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:177855600-177858200	Enhancers	Pancreas	Pancrea
6	chr5:177855800-177857600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:177856000-177861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:177856400-177857600	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr5:177856400-177857600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr5:177856400-177861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:177856600-177857800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:177856600-177861000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:177856800-177857400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:177856800-177861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:177856800-177861600	Weak transcription	Brain Angular Gyrus	brain
16	chr5:177856800-177861600	Weak transcription	Fetal Heart	heart
17	chr5:177856800-177861800	Weak transcription	Left Ventricle	heart
18	chr5:177856800-177887200	Weak transcription	Right Atrium	heart
19	chr5:177857000-177859400	Weak transcription	Right Ventricle	heart
20	chr5:177857000-177859600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:177857000-177861600	Weak transcription	Psoas Muscle	Psoas
22	chr5:177857000-177862600	Weak transcription	Gastric	stomach
23	chr5:177857000-177863800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:177857200-177858000	Weak transcription	Lung	lung
25	chr5:177857200-177858400	Weak transcription	Fetal Stomach	stomach
26	chr5:177857200-177859200	Strong transcription	Fetal Thymus	thymus
27	chr5:177857200-177859400	Weak transcription	Liver	Liver
28	chr5:177857200-177859600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:177857200-177862000	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links