Variant report

Variant	rs2803168
Chromosome Location	chr1:77999946-77999947
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	chr1:76619553..76620451-chr1:77999109..77999974,2	K562	blood:
2	chr1:77999652..78002822-chr1:78004325..78005902,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1013399	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782654	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873949	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873950	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10873951	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11162362	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162364	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162365	0.90[ASN][1000 genomes]
rs11162369	0.83[ASN][1000 genomes]
rs11162372	0.81[ASN][1000 genomes]
rs12071212	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074409	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12095064	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142671	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs12717767	0.90[ASN][1000 genomes]
rs12724560	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565850	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565851	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1565852	0.86[ASN][1000 genomes]
rs1962523	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1976334	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029768	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133202	0.90[ASN][1000 genomes]
rs2172727	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2647486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647487	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278854	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2803136	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34773766	0.89[ASN][1000 genomes]
rs3509	0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs371076	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs3738079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767030	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap]
rs3767032	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767033	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4245658	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4589153	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600093	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949657	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949658	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949659	0.89[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949807	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949808	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949809	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4949811	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4949813	0.91[ASN][1000 genomes]
rs4949816	0.94[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6603952	0.80[ASN][1000 genomes]
rs6603953	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6603955	0.90[ASN][1000 genomes]
rs6667519	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs6667803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675743	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6692369	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695989	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696083	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs728741	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7513619	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7519476	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524147	0.94[ASN][1000 genomes]
rs7524866	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7531286	0.82[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545544	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551729	1.00[ASW][hapmap];1.00[CEU][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];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872342	0.83[CHD][hapmap]
rs962388	0.91[ASN][1000 genomes]
rs9787153	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2803168	AK5	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77996800-78001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:77998200-78000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:77998200-78000000	Enhancers	NHDF-Ad	bronchial
6	chr1:77998200-78000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:77998200-78000200	Enhancers	Brain Angular Gyrus	brain
8	chr1:77998200-78000400	Enhancers	Brain Hippocampus Middle	brain
9	chr1:77998200-78000600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:77998200-78005000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:77998400-78000600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:77999000-78000000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:77999000-78000000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:77999200-78000000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:77999200-78000000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:77999200-78000000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:77999200-78000000	Enhancers	Liver	Liver
18	chr1:77999200-78000600	Enhancers	NHLF	lung
19	chr1:77999200-78000800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:77999200-78001000	Enhancers	HUVEC	blood vessel
21	chr1:77999200-78002000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:77999200-78004600	Enhancers	NH-A	brain
23	chr1:77999400-78000000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:77999400-78000000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:77999400-78000000	Enhancers	Adipose Nuclei	Adipose
26	chr1:77999400-78000000	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr1:77999400-78000000	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:77999400-78000000	Enhancers	Fetal Kidney	kidney
29	chr1:77999400-78000000	Enhancers	HSMM	muscle
30	chr1:77999400-78000000	Enhancers	HSMMtube	muscle
31	chr1:77999400-78000200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:77999400-78000200	Enhancers	Brain Substantia Nigra	brain
33	chr1:77999400-78000200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr1:77999400-78001600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:77999600-78000000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr1:77999600-78000000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr1:77999600-78000000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr1:77999600-78000000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:77999600-78000000	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:77999600-78000000	Enhancers	Fetal Intestine Small	intestine
41	chr1:77999600-78000000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:77999600-78000000	Enhancers	Hela-S3	cervix
43	chr1:77999600-78000000	Enhancers	HMEC	breast
44	chr1:77999600-78000000	Flanking Active TSS	Osteobl	bone
45	chr1:77999600-78000200	Enhancers	Primary B cells from cord blood	blood
46	chr1:77999600-78000200	Flanking Active TSS	HepG2	liver
47	chr1:77999600-78000800	Weak transcription	Primary T cells from cord blood	blood
48	chr1:77999600-78001200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:77999600-78003800	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:77999600-78004000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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