Variant report

Variant	rs423906
Chromosome Location	chr5:79351735-79351736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79350174..79351742-chr5:79371407..79373227,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs194375	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2434270	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2434273	0.83[EUR][1000 genomes]
rs2434309	0.83[EUR][1000 genomes]
rs2434310	0.83[EUR][1000 genomes]
rs2434311	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2434314	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434315	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434318	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2434319	0.84[EUR][1000 genomes]
rs2438604	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2438605	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2438607	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2438611	0.84[EUR][1000 genomes]
rs2438612	0.84[EUR][1000 genomes]
rs2438613	0.84[EUR][1000 genomes]
rs2438614	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2438617	0.83[EUR][1000 genomes]
rs2438618	0.83[EUR][1000 genomes]
rs2438650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2438651	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2451933	0.84[EUR][1000 genomes]
rs2451940	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs256440	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256441	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256444	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256446	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256447	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256448	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256451	0.83[EUR][1000 genomes]
rs366553	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs391521	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs398774	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs401302	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs434409	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv882219	chr5:79320677-79354147	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882222	chr5:79321439-79354147	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882223	chr5:79330559-79357117	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv882224	chr5:79335975-79351735	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv882225	chr5:79342519-79353428	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv882226	chr5:79346880-79353428	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv882227	chr5:79347336-79351735	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv882228	chr5:79347336-79353428	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv882229	chr5:79348759-79353428	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv882230	chr5:79351544-79354647	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79338200-79363600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:79338200-79367600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:79338400-79355200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:79339200-79354600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:79340000-79363400	Weak transcription	Left Ventricle	heart
6	chr5:79344200-79355200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:79345200-79364200	Weak transcription	Right Ventricle	heart
8	chr5:79347800-79355600	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:79348200-79366400	Weak transcription	Brain Substantia Nigra	brain
10	chr5:79350600-79363200	Weak transcription	Psoas Muscle	Psoas
11	chr5:79351000-79352000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:79351000-79352400	Enhancers	NHEK	skin
13	chr5:79351200-79351800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:79351200-79352000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr5:79351200-79352000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:79351200-79352000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:79351200-79352200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr5:79351400-79351800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:79351400-79351800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr5:79351400-79351800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr5:79351400-79351800	Flanking Active TSS	HMEC	breast
22	chr5:79351400-79352000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:79351400-79352000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr5:79351400-79352000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:79351400-79352000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:79351400-79352000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr5:79351400-79352000	Enhancers	GM12878-XiMat	blood
28	chr5:79351400-79352200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr5:79351400-79352200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:79351600-79352000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:79351600-79352200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:79351600-79352400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr5:79351600-79352600	Enhancers	Fetal Heart	heart
34	chr5:79351600-79379200	Weak transcription	Pancreas	Pancrea

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