Variant report

Variant	rs71643439
Chromosome Location	chr1:217216380-217216381
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	chr1:217215201..217218103-chr1:217218640..217221582,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11572415	0.96[ASN][1000 genomes]
rs11572427	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11572435	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11577589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11585218	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11585774	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12723476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12724974	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12731437	0.81[EUR][1000 genomes]
rs12738035	0.90[AFR][1000 genomes]
rs12741457	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12747869	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12750129	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12756498	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12759546	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12759584	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17044977	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17636663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17686743	0.90[AFR][1000 genomes]
rs17686866	0.90[AFR][1000 genomes]
rs1890555	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34056739	0.90[AFR][1000 genomes]
rs34096624	0.90[AFR][1000 genomes]
rs34493634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34904258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35185630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35409092	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35701761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4846800	0.90[AFR][1000 genomes]
rs4846801	0.90[AFR][1000 genomes]
rs6681177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6684076	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217204800-217226000	Weak transcription	Fetal Kidney	kidney
2	chr1:217212000-217223200	Weak transcription	Gastric	stomach
3	chr1:217212600-217223000	Weak transcription	Pancreas	Pancrea
4	chr1:217212600-217224800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:217213400-217240600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:217214600-217216800	Enhancers	Fetal Muscle Leg	muscle
7	chr1:217214800-217216800	Enhancers	Brain Hippocampus Middle	brain
8	chr1:217215000-217216400	Enhancers	Fetal Brain Male	brain
9	chr1:217215200-217216600	Enhancers	Right Atrium	heart
10	chr1:217215400-217216400	Enhancers	Fetal Brain Female	brain
11	chr1:217215400-217216800	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr1:217215400-217217000	Enhancers	Brain Anterior Caudate	brain
13	chr1:217215400-217226600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:217215600-217216400	Enhancers	Fetal Lung	lung
15	chr1:217215600-217216400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:217215600-217216600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:217215600-217216600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:217215600-217216600	Enhancers	Stomach Smooth Muscle	stomach
19	chr1:217215600-217216800	Enhancers	Brain Substantia Nigra	brain
20	chr1:217215600-217217000	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:217215800-217216400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:217215800-217216400	Enhancers	Fetal Stomach	stomach
23	chr1:217215800-217216600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:217215800-217216600	Enhancers	HSMMtube	muscle
25	chr1:217215800-217216800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:217215800-217216800	Enhancers	Brain Angular Gyrus	brain
27	chr1:217215800-217217000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:217216000-217217400	Weak transcription	Left Ventricle	heart
29	chr1:217216000-217221000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:217216200-217216600	Enhancers	H9 Cell Line	embryonic stem cell
31	chr1:217216200-217216600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:217216200-217216600	Flanking Active TSS	Fetal Heart	heart
33	chr1:217216200-217216800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links