Variant report

Variant	rs2272801
Chromosome Location	chr1:169366516-169366517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1028180	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753786	0.83[CHB][hapmap]
rs10800447	0.83[CHB][hapmap]
rs1080268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919173	0.89[CHB][hapmap]
rs1208373	0.96[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs12121994	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12143193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12145146	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12145226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12729761	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12733001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12733037	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12733626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12744859	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12745541	0.87[EUR][1000 genomes]
rs12748624	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs12751929	0.83[EUR][1000 genomes]
rs12752953	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1517745	0.89[CHB][hapmap]
rs1533518	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533519	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16828165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16862081	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs16862097	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16862133	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862153	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862176	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862217	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1883167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2037249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066001	1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2203743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300158	0.83[CHB][hapmap]
rs2300160	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2420015	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2420016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34057682	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34373126	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34599582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34640648	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34858340	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34930817	0.83[EUR][1000 genomes]
rs35171152	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35406371	0.83[EUR][1000 genomes]
rs35686518	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35918529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36040633	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3753299	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs3765229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766076	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3766078	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766090	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3766097	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4140538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4140539	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs41442344	1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4551642	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4590731	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57295069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58809384	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66512221	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672589	0.89[CHB][hapmap]
rs6675220	1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs66937324	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67795749	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724048	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs72637232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929133	0.94[CHB][hapmap];0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:169349400-169367400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:169350200-169366800	Weak transcription	HSMMtube	muscle
5	chr1:169350200-169368600	Weak transcription	Colonic Mucosa	Colon
6	chr1:169352800-169367400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:169353000-169369800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:169354000-169370000	Weak transcription	Aorta	Aorta
9	chr1:169354800-169370600	Weak transcription	Fetal Kidney	kidney
10	chr1:169357000-169368200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:169358200-169368000	Weak transcription	Esophagus	oesophagus
12	chr1:169359200-169366800	Weak transcription	Fetal Brain Male	brain
13	chr1:169359200-169368400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169359600-169369800	Weak transcription	NHDF-Ad	bronchial
15	chr1:169360600-169372200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:169360800-169367400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:169360800-169367800	Weak transcription	Psoas Muscle	Psoas
18	chr1:169360800-169369200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:169360800-169370600	Weak transcription	NHLF	lung
20	chr1:169360800-169395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:169361000-169366600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:169361200-169366800	Weak transcription	Hela-S3	cervix
23	chr1:169361400-169368000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:169361400-169369400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:169361800-169366800	Weak transcription	Brain Substantia Nigra	brain
26	chr1:169362200-169367000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:169362200-169367400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:169362200-169370000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:169362200-169370000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:169362200-169371200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:169362400-169368000	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:169362400-169368800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:169362400-169369800	Weak transcription	Fetal Thymus	thymus
34	chr1:169362400-169370000	Weak transcription	Brain Germinal Matrix	brain
35	chr1:169362400-169370000	Weak transcription	Fetal Brain Female	brain
36	chr1:169362600-169369600	Weak transcription	Primary T cells from cord blood	blood
37	chr1:169363200-169368200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:169363400-169368800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:169363400-169371200	Weak transcription	Ovary	ovary
40	chr1:169363600-169367800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:169363600-169368800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:169363800-169367000	Weak transcription	NHEK	skin
43	chr1:169363800-169367400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:169363800-169367800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:169363800-169368600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:169364000-169369000	Weak transcription	Brain Angular Gyrus	brain
47	chr1:169364200-169366800	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:169364200-169367200	Weak transcription	Primary B cells from cord blood	blood
49	chr1:169364200-169368600	Weak transcription	HMEC	breast
50	chr1:169364400-169366800	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links