Variant report

Variant	rs278854
Chromosome Location	chr1:78132534-78132535
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78129208..78133797-chr1:78137082..78139912,5	K562	blood:
2	chr1:78131407..78136393-chr1:78144019..78149939,7	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1038983	0.94[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10782654	0.81[ASN][1000 genomes]
rs10873949	0.81[ASN][1000 genomes]
rs10873950	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs10873951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10873955	0.94[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs11162362	0.81[ASN][1000 genomes]
rs11162364	0.81[ASN][1000 genomes]
rs11162365	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11162366	0.84[EUR][1000 genomes]
rs11162369	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162372	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11162378	0.81[GIH][hapmap]
rs11162380	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162386	0.94[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs11162387	0.87[CEU][hapmap]
rs11578805	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1166584	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1166586	0.82[CEU][hapmap]
rs1166588	0.88[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs12026939	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12074409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12128041	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12142671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12717767	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12724560	0.81[ASN][1000 genomes]
rs1389789	0.81[GIH][hapmap]
rs1389790	0.83[GIH][hapmap]
rs1565850	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1565851	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1565852	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962523	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1977900	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2029768	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.81[ASN][1000 genomes]
rs203229	0.81[GIH][hapmap]
rs2147318	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2172727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.81[ASN][1000 genomes]
rs2274123	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2647486	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs278833	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278836	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278837	0.81[GIH][hapmap]
rs278838	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278842	0.81[GIH][hapmap]
rs278843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278845	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278847	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278850	0.81[GIH][hapmap]
rs278852	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278857	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278858	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278859	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278862	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278864	0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2803136	0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2803168	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs3509	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs366467	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs370335	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs371076	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767030	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs3767037	0.81[GIH][hapmap]
rs4245658	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4589153	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4600093	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949658	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949659	0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4949661	0.85[EUR][1000 genomes]
rs4949808	0.81[ASN][1000 genomes]
rs4949809	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4949811	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs4949813	0.86[ASN][1000 genomes]
rs4949814	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs4949816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4949818	0.81[GIH][hapmap]
rs4949822	0.80[AMR][1000 genomes]
rs574973	0.81[GIH][hapmap]
rs6603955	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6603956	0.94[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6657290	0.94[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6661656	0.83[GIH][hapmap]
rs6667519	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6667803	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6670660	0.85[EUR][1000 genomes]
rs6672200	0.94[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6674638	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6675743	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6687501	0.81[GIH][hapmap]
rs6691317	0.85[EUR][1000 genomes]
rs6693100	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6695989	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6696083	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6698151	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs728741	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs7513619	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7519476	0.81[ASN][1000 genomes]
rs7521042	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7524866	0.93[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7531286	0.89[CHB][hapmap]
rs7545175	0.85[EUR][1000 genomes]
rs7545544	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7551211	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7551729	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7552291	0.94[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs872342	0.83[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs962388	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9662527	0.94[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][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	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	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs278854	AK5	cis	parietal	SCAN
rs278854	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78099000-78147200	Weak transcription	Gastric	stomach
2	chr1:78100800-78133200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:78107600-78146000	Weak transcription	Fetal Kidney	kidney
4	chr1:78110400-78138000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:78111200-78147200	Weak transcription	Esophagus	oesophagus
6	chr1:78111400-78137400	Weak transcription	HUVEC	blood vessel
7	chr1:78111400-78137600	Weak transcription	Hela-S3	cervix
8	chr1:78112200-78139000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:78114800-78135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:78114800-78135800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:78116800-78144600	Weak transcription	NHEK	skin
12	chr1:78117200-78144400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:78117400-78134800	Weak transcription	Osteobl	bone
14	chr1:78117400-78137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:78117400-78138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:78117400-78141800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:78117400-78147200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:78117600-78137400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:78117600-78137600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:78117600-78138200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:78117600-78139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:78117600-78146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:78117600-78147200	Weak transcription	Thymus	Thymus
24	chr1:78118200-78137200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:78118600-78146000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:78119000-78139000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:78119000-78145600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:78119000-78146000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:78119400-78147200	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:78120800-78147200	Weak transcription	Lung	lung
31	chr1:78121400-78133400	Weak transcription	Primary T cells from cord blood	blood
32	chr1:78121400-78137600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:78121400-78137600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:78121600-78137600	Weak transcription	A549	lung
35	chr1:78123800-78139400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:78124600-78146000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:78125800-78136000	Weak transcription	Spleen	Spleen
38	chr1:78126400-78133200	Weak transcription	GM12878-XiMat	blood
39	chr1:78126400-78134000	Weak transcription	HSMM	muscle
40	chr1:78127000-78135400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:78127000-78146400	Weak transcription	Primary B cells from cord blood	blood
42	chr1:78127400-78139800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:78128400-78133200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:78128800-78133200	Weak transcription	Fetal Intestine Large	intestine
45	chr1:78128800-78137200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:78128800-78141000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:78128800-78141800	Weak transcription	Fetal Intestine Small	intestine
48	chr1:78130400-78132600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:78130600-78134200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr1:78131000-78133200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links