Variant report

Variant	rs1159520
Chromosome Location	chr21:40899128-40899129
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40899001..40900930-chr21:40949117..40954040,4	MCF-7	breast:
2	chr17:58676920..58679368-chr21:40897816..40900340,2	MCF-7	breast:
3	chr21:40897577..40899637-chr21:40983586..40986470,3	MCF-7	breast:
4	chr21:40898411..40901316-chr21:40977081..40979354,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGR-1	chr21:40898286-40901782	NONHSAT082198

Variant related genes	Relation type
ENSG00000170836	Chromatin interaction
ENSG00000184809	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16997808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7277174	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7283782	1.00[MEX][hapmap]
rs73904046	0.84[AFR][1000 genomes]
rs73906060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73906062	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8126968	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8131479	0.81[YRI][hapmap];0.93[AMR][1000 genomes]
rs8134055	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40877400-40899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr21:40880200-40899800	Weak transcription	Fetal Muscle Leg	muscle
3	chr21:40888200-40907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr21:40894400-40901600	Enhancers	Pancreas	Pancrea
5	chr21:40895600-40899600	Weak transcription	Fetal Stomach	stomach
6	chr21:40895800-40899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:40895800-40909600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr21:40896000-40899200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr21:40896000-40899800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr21:40896000-40903000	Weak transcription	Brain Substantia Nigra	brain
11	chr21:40896200-40899200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr21:40896200-40899600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr21:40896200-40899800	Weak transcription	Brain Hippocampus Middle	brain
14	chr21:40896200-40899800	Weak transcription	Colonic Mucosa	Colon
15	chr21:40896200-40900800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr21:40896800-40899800	Weak transcription	Fetal Brain Male	brain
17	chr21:40897600-40899200	Weak transcription	Adipose Nuclei	Adipose
18	chr21:40897600-40899600	Weak transcription	Brain Anterior Caudate	brain
19	chr21:40897600-40899800	Weak transcription	Spleen	Spleen
20	chr21:40897800-40899200	Weak transcription	Lung	lung
21	chr21:40898000-40899800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:40898200-40899200	Enhancers	Fetal Heart	heart
23	chr21:40898600-40899200	Enhancers	HepG2	liver
24	chr21:40898600-40899600	Enhancers	Liver	Liver
25	chr21:40898600-40900800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr21:40898800-40899600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr21:40898800-40900200	Enhancers	Right Atrium	heart
28	chr21:40898800-40900400	Enhancers	Placenta	Placenta
29	chr21:40898800-40900400	Enhancers	Right Ventricle	heart
30	chr21:40898800-40900600	Enhancers	Left Ventricle	heart
31	chr21:40898800-40900800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr21:40899000-40899600	Enhancers	Small Intestine	intestine
33	chr21:40899000-40900600	Enhancers	Fetal Intestine Large	intestine
34	chr21:40899000-40901000	Enhancers	Fetal Intestine Small	intestine
35	chr21:40899000-40901400	Enhancers	Stomach Mucosa	stomach

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