Variant report

Variant	rs10179020
Chromosome Location	chr2:172698853-172698854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172698622..172703344-chr2:172704675..172709046,4	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10177679	0.93[EUR][1000 genomes]
rs10184770	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10185633	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10191399	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10196521	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10201520	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1022358	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10432474	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10930493	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10930501	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1105264	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11676484	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11677573	0.82[AMR][1000 genomes]
rs11903123	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11903410	0.83[AMR][1000 genomes]
rs12464262	0.90[ASN][1000 genomes]
rs12467010	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12471160	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12473516	0.88[EUR][1000 genomes]
rs12478189	0.82[ASN][1000 genomes]
rs12479374	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12619137	0.80[AFR][1000 genomes]
rs12692971	0.86[ASN][1000 genomes]
rs13012103	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13031370	0.83[AMR][1000 genomes]
rs13399316	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1400816	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515812	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1517678	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1543168	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554165	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1607253	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859721	0.90[ASN][1000 genomes]
rs17580984	0.90[ASN][1000 genomes]
rs17614989	0.90[ASN][1000 genomes]
rs17615013	0.90[ASN][1000 genomes]
rs1850031	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1878583	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1982288	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1996425	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028670	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2028671	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2028672	0.91[EUR][1000 genomes]
rs2037164	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2176466	0.84[AFR][1000 genomes]
rs2292813	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292814	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2357064	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2357207	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2357208	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28372952	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs312917	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3770443	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770444	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770453	0.82[AMR][1000 genomes]
rs3770457	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3791343	0.88[EUR][1000 genomes]
rs3821092	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821094	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821096	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4507064	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668416	0.80[AFR][1000 genomes]
rs4668417	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58565148	0.90[ASN][1000 genomes]
rs60706248	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6433313	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433315	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433316	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6433317	0.81[AFR][1000 genomes]
rs6433318	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6433322	0.83[AMR][1000 genomes]
rs6707142	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6714214	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6726050	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6733123	0.82[AMR][1000 genomes]
rs6742905	0.98[EUR][1000 genomes]
rs6753551	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6753859	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7371631	0.83[AMR][1000 genomes]
rs7574090	0.92[ASN][1000 genomes]
rs7574711	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7583860	0.82[AMR][1000 genomes]
rs7588025	0.81[AFR][1000 genomes]
rs7588351	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7597525	0.96[EUR][1000 genomes]
rs7598232	0.83[AMR][1000 genomes]
rs7604933	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs925881	0.83[AFR][1000 genomes]
rs9287948	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs949548	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9636293	0.84[AFR][1000 genomes]
rs970948	0.87[AMR][1000 genomes];0.94[ASN][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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172689400-172712200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:172690200-172720600	Weak transcription	Gastric	stomach
3	chr2:172690200-172721000	Weak transcription	Aorta	Aorta
4	chr2:172690200-172750200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:172690600-172712000	Weak transcription	Hela-S3	cervix
6	chr2:172691400-172738600	Weak transcription	Esophagus	oesophagus
7	chr2:172691800-172702000	Weak transcription	HMEC	breast
8	chr2:172692200-172714400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:172692200-172733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:172693200-172728000	Weak transcription	Colonic Mucosa	Colon
11	chr2:172693400-172711800	Weak transcription	HSMMtube	muscle
12	chr2:172693400-172713200	Weak transcription	NH-A	brain
13	chr2:172693400-172734800	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:172693600-172700000	Weak transcription	Placenta	Placenta
15	chr2:172693600-172700000	Weak transcription	Thymus	Thymus
16	chr2:172693600-172708200	Weak transcription	Fetal Heart	heart
17	chr2:172693600-172709000	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:172693600-172712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:172693600-172712200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:172693600-172713200	Weak transcription	Fetal Brain Male	brain
21	chr2:172693600-172724200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:172693600-172734400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:172693600-172734600	Weak transcription	HSMM	muscle
24	chr2:172693800-172700800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:172693800-172701200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:172693800-172704200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:172693800-172704600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:172693800-172708800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:172693800-172710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:172693800-172710400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:172693800-172710400	Weak transcription	A549	lung
32	chr2:172693800-172711800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:172693800-172712000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:172693800-172715000	Weak transcription	NHLF	lung
35	chr2:172693800-172719000	Weak transcription	Psoas Muscle	Psoas
36	chr2:172693800-172720600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:172693800-172721000	Weak transcription	Brain Anterior Caudate	brain
38	chr2:172693800-172721000	Weak transcription	Spleen	Spleen
39	chr2:172693800-172725800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:172693800-172727000	Weak transcription	Fetal Kidney	kidney
41	chr2:172693800-172732600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:172693800-172734600	Weak transcription	Right Ventricle	heart
43	chr2:172694000-172699800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:172694000-172704600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:172694000-172708400	Weak transcription	NHDF-Ad	bronchial
46	chr2:172694000-172711200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:172694000-172712400	Weak transcription	K562	blood
48	chr2:172694000-172724200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:172694000-172724200	Weak transcription	Brain Germinal Matrix	brain
50	chr2:172694000-172732800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links