Variant report

Variant	rs1873878
Chromosome Location	chr1:95165873-95165874
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10218699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10218700	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10218701	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10493877	0.82[AMR][1000 genomes]
rs10782990	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10782991	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10874879	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10874880	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10874881	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10874882	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10874883	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10874884	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11165209	0.80[AMR][1000 genomes]
rs11165210	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs11165211	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs11165212	0.82[AMR][1000 genomes]
rs11165215	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11165217	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11165218	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11165219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12085094	0.82[AMR][1000 genomes]
rs12089652	0.82[AMR][1000 genomes]
rs12116841	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12117807	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120217	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12127717	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12128735	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138432	0.82[AMR][1000 genomes]
rs12145601	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12409876	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12409905	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12409906	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12736683	0.82[AMR][1000 genomes]
rs12739283	0.82[AMR][1000 genomes]
rs12739612	0.82[AMR][1000 genomes]
rs12739646	0.82[AMR][1000 genomes]
rs12740172	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12750395	0.82[AMR][1000 genomes]
rs12756850	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12756853	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12757140	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12757198	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12757945	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12758342	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12760023	0.82[AMR][1000 genomes]
rs12760228	0.82[AMR][1000 genomes]
rs12760666	0.82[AMR][1000 genomes]
rs1493275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493277	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1891871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994850	0.82[AMR][1000 genomes]
rs2040074	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2040075	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2040076	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2040077	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2391384	0.81[AMR][1000 genomes]
rs2391385	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs2391387	0.84[AMR][1000 genomes]
rs2893273	0.82[AMR][1000 genomes]
rs3956597	0.82[AMR][1000 genomes]
rs4000655	0.82[AMR][1000 genomes]
rs4000656	0.82[AMR][1000 genomes]
rs4000657	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4000658	0.92[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4240958	0.83[AMR][1000 genomes]
rs4240959	0.82[AMR][1000 genomes]
rs4240960	0.92[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4274076	0.82[AMR][1000 genomes]
rs4319342	0.82[AMR][1000 genomes]
rs4338361	0.82[AMR][1000 genomes]
rs4394665	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4567290	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4598496	0.82[AMR][1000 genomes]
rs4847337	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs4847338	0.82[AMR][1000 genomes]
rs4847339	0.82[AMR][1000 genomes]
rs4847340	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847341	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847342	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847343	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663811	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7412205	0.83[AMR][1000 genomes]
rs7416454	0.83[AMR][1000 genomes]
rs7546581	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7546594	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7546688	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs841340	0.92[CEU][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs859337	0.81[EUR][1000 genomes]
rs865779	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923815	0.82[AMR][1000 genomes]
rs964213	0.82[AMR][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	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv871001	chr1:95128546-95171891	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv871916	chr1:95143999-95189230	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001043	chr1:95158042-95185906	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1873878	HSP90B3P	cis	cerebellum	SCAN
rs1873878	DNTTIP2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95142800-95167800	Weak transcription	Pancreas	Pancrea
2	chr1:95152800-95195000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:95153000-95173000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:95153400-95167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:95155800-95173200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:95160200-95166400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:95160400-95167800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:95163200-95169000	Enhancers	NHDF-Ad	bronchial
9	chr1:95163400-95166000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:95163600-95166200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:95163800-95167800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:95164000-95167600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:95164200-95166000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:95164200-95168000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:95164400-95167000	Weak transcription	Stomach Mucosa	stomach
16	chr1:95164400-95167600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:95164400-95167600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:95164400-95167800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:95164400-95167800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:95164400-95168000	Weak transcription	HSMM	muscle
21	chr1:95164600-95167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:95164600-95167800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:95164600-95167800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:95164600-95168600	Enhancers	HepG2	liver
25	chr1:95164800-95171000	Weak transcription	HSMMtube	muscle
26	chr1:95164800-95174000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:95165000-95167600	Weak transcription	Fetal Kidney	kidney
28	chr1:95165000-95167800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:95165000-95167800	Weak transcription	NHLF	lung
30	chr1:95165000-95171000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:95165000-95173200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:95165000-95175400	Weak transcription	NH-A	brain
33	chr1:95165200-95166000	Weak transcription	Fetal Intestine Small	intestine
34	chr1:95165200-95166600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:95165200-95166600	Weak transcription	Ovary	ovary
36	chr1:95165200-95167400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:95165200-95167600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:95165200-95167800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:95165200-95167800	Weak transcription	Placenta	Placenta
40	chr1:95165400-95167800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:95165600-95167000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:95165800-95166000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:95165800-95166000	Enhancers	Right Atrium	heart
44	chr1:95165800-95167600	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links