Variant report

Variant	rs517901
Chromosome Location	chr1:72300502-72300503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11209852	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11209853	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs11209854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12037610	0.89[EUR][1000 genomes]
rs1350648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1426178	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1814055	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs3909665	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490859	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs495411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs508954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs510012	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs514435	0.80[CHB][hapmap]
rs518523	0.82[JPT][hapmap]
rs545538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs546741	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs554161	0.80[CHB][hapmap]
rs595910	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs629079	0.80[CHB][hapmap]
rs648556	0.80[CHB][hapmap]
rs6659202	0.88[CEU][hapmap]
rs6683448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526542	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7529181	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2762150	chr1:72271227-72395953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72293200-72301800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:72294800-72302200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:72294800-72302400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:72294800-72302600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:72295200-72302600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:72295600-72301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:72295600-72302400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:72298400-72302800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:72299400-72300600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr1:72299400-72301000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:72299600-72304600	Enhancers	Fetal Heart	heart
12	chr1:72300000-72300800	Enhancers	Pancreas	Pancrea
13	chr1:72300000-72300800	Enhancers	Small Intestine	intestine
14	chr1:72300000-72301000	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:72300000-72301000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:72300000-72301000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:72300200-72300600	Enhancers	Aorta	Aorta
18	chr1:72300200-72300800	Enhancers	Fetal Stomach	stomach
19	chr1:72300200-72300800	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:72300200-72301000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:72300200-72301000	Enhancers	Fetal Intestine Small	intestine
22	chr1:72300400-72300600	Enhancers	Brain Hippocampus Middle	brain
23	chr1:72300400-72300800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr1:72300400-72300800	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr1:72300400-72300800	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:72300400-72301200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:72300400-72301400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links