Variant report

Variant	rs2102638
Chromosome Location	chr1:227456453-227456454
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227454247..227456630-chr1:227461574..227463571,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10429872	0.91[ASN][1000 genomes]
rs10495255	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10737428	0.85[ASN][1000 genomes]
rs10753433	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10799409	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10799410	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10916106	0.80[ASN][1000 genomes]
rs10916108	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10916111	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916118	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916122	0.85[ASN][1000 genomes]
rs12065126	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12137591	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12565871	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566059	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569227	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34084723	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34875093	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35738984	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3795457	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4339829	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653812	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653823	0.82[ASN][1000 genomes]
rs4653824	0.83[ASN][1000 genomes]
rs4653825	0.82[ASN][1000 genomes]
rs60197034	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6656653	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6682120	0.85[ASN][1000 genomes]
rs6684784	0.85[ASN][1000 genomes]
rs6684803	0.84[ASN][1000 genomes]
rs6685106	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6692294	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6697272	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6700730	0.81[AMR][1000 genomes]
rs72759337	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7516326	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519752	0.91[ASN][1000 genomes]
rs7537038	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs955704	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
4	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
5	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
6	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:227440000-227456600	Weak transcription	HepG2	liver
10	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
11	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:227445800-227458400	Weak transcription	NHEK	skin
13	chr1:227447000-227456800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:227448600-227457200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:227449600-227473600	Weak transcription	NH-A	brain
17	chr1:227449800-227465200	Weak transcription	K562	blood
18	chr1:227452800-227463800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:227453000-227468600	Weak transcription	Lung	lung
20	chr1:227453600-227457200	Enhancers	Brain Substantia Nigra	brain
21	chr1:227454200-227470400	Weak transcription	Ovary	ovary
22	chr1:227455000-227457200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:227455200-227457200	Enhancers	Brain Anterior Caudate	brain
24	chr1:227455400-227456600	Enhancers	Left Ventricle	heart
25	chr1:227455400-227456600	Enhancers	Right Ventricle	heart
26	chr1:227455400-227456800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:227455400-227457000	Enhancers	Brain Angular Gyrus	brain
28	chr1:227455600-227458600	Enhancers	Liver	Liver
29	chr1:227455800-227457000	Enhancers	Adipose Nuclei	Adipose
30	chr1:227456000-227456800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:227456000-227458400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:227456000-227458400	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:227456200-227456800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:227456400-227456600	Enhancers	Stomach Mucosa	stomach
35	chr1:227456400-227456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:227456400-227457000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:227456400-227457000	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links