Variant report

Variant	rs28491817
Chromosome Location	chr2:233703903-233703904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10176930	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10178713	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207739	0.88[ASN][1000 genomes]
rs10933407	0.80[EUR][1000 genomes]
rs10933408	0.80[EUR][1000 genomes]
rs11679581	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684636	0.88[ASN][1000 genomes]
rs11685169	0.80[EUR][1000 genomes]
rs11689661	0.88[ASN][1000 genomes]
rs11694434	0.80[EUR][1000 genomes]
rs11695762	0.86[EUR][1000 genomes]
rs11904619	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12328140	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12328151	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12694916	0.80[EUR][1000 genomes]
rs12988087	0.84[ASN][1000 genomes]
rs12992588	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13012585	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13035517	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13383733	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13386650	0.80[EUR][1000 genomes]
rs13387762	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13408229	0.88[ASN][1000 genomes]
rs13412034	0.80[EUR][1000 genomes]
rs13412513	0.80[EUR][1000 genomes]
rs13424896	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13425525	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13425918	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429857	0.80[EUR][1000 genomes]
rs1446307	0.83[EUR][1000 genomes]
rs2044450	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2048866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2289914	0.83[EUR][1000 genomes]
rs2289915	0.83[EUR][1000 genomes]
rs2292724	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2292725	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2293782	0.83[EUR][1000 genomes]
rs2305139	0.86[EUR][1000 genomes]
rs34063802	0.83[EUR][1000 genomes]
rs34652626	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34832091	0.81[EUR][1000 genomes]
rs35141217	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35778045	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35785837	0.80[EUR][1000 genomes]
rs35928329	0.80[EUR][1000 genomes]
rs41266951	0.83[EUR][1000 genomes]
rs56054779	0.83[EUR][1000 genomes]
rs62193305	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73005582	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9288675	0.80[EUR][1000 genomes]
rs9288676	0.83[EUR][1000 genomes]
rs9808146	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9973586	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460134	chr2:233639909-233714686	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv584696	chr2:233639909-233714686	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689000-233713000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:233691200-233717200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:233695400-233705600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:233696400-233714200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:233698400-233723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:233699200-233704000	Weak transcription	Aorta	Aorta
10	chr2:233699200-233704000	Weak transcription	Psoas Muscle	Psoas
11	chr2:233699200-233704600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:233699200-233712000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:233699200-233717000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:233699800-233717000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:233700000-233704000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:233700000-233704600	Strong transcription	Fetal Stomach	stomach
17	chr2:233700000-233705200	Weak transcription	Fetal Brain Male	brain
18	chr2:233700200-233704600	Genic enhancers	Duodenum Mucosa	Duodenum
19	chr2:233700600-233708800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:233700600-233714200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:233700800-233707200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:233701000-233707400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:233701400-233705400	Strong transcription	Brain Germinal Matrix	brain
25	chr2:233701600-233704600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr2:233701600-233704600	Genic enhancers	Rectal Mucosa Donor 29	rectum
27	chr2:233701600-233704600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:233701800-233707400	Weak transcription	Right Atrium	heart
29	chr2:233701800-233717000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:233702000-233704000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:233702000-233704400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:233702000-233704400	Weak transcription	Ovary	ovary
33	chr2:233702000-233704400	Weak transcription	HSMMtube	muscle
34	chr2:233702000-233704600	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:233702000-233704600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:233702000-233706400	Weak transcription	Left Ventricle	heart
37	chr2:233702000-233706800	Weak transcription	Esophagus	oesophagus
38	chr2:233702000-233706800	Weak transcription	Lung	lung
39	chr2:233702200-233704200	Genic enhancers	Fetal Thymus	thymus
40	chr2:233702200-233704400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:233702200-233704800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:233702200-233704800	Enhancers	Hela-S3	cervix
43	chr2:233702400-233704000	Enhancers	Primary B cells from cord blood	blood
44	chr2:233702400-233704000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr2:233702400-233704000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:233702400-233704000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr2:233702400-233704400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:233702400-233704600	Genic enhancers	NHEK	skin
49	chr2:233702400-233704800	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr2:233702400-233704800	Enhancers	HUVEC	blood vessel

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