Variant report

Variant	rs2987871
Chromosome Location	chr1:174786055-174786056
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10912809	1.00[EUR][1000 genomes]
rs10912815	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912816	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912818	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912819	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912847	1.00[EUR][1000 genomes]
rs10912851	1.00[EUR][1000 genomes]
rs10912858	1.00[EUR][1000 genomes]
rs10912864	1.00[EUR][1000 genomes]
rs11806870	1.00[EUR][1000 genomes]
rs12057161	1.00[EUR][1000 genomes]
rs12057359	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066268	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066421	1.00[EUR][1000 genomes]
rs12067791	1.00[EUR][1000 genomes]
rs12068625	1.00[EUR][1000 genomes]
rs12069689	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070082	1.00[EUR][1000 genomes]
rs12072909	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075193	1.00[EUR][1000 genomes]
rs12077283	1.00[EUR][1000 genomes]
rs12080070	1.00[EUR][1000 genomes]
rs12080242	1.00[EUR][1000 genomes]
rs12084999	1.00[EUR][1000 genomes]
rs12088650	1.00[EUR][1000 genomes]
rs12096717	1.00[EUR][1000 genomes]
rs1231828	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1329280	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1612104	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1618234	1.00[EUR][1000 genomes]
rs1653631	1.00[EUR][1000 genomes]
rs1653633	1.00[EUR][1000 genomes]
rs1653637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847457	1.00[EUR][1000 genomes]
rs173000	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1754356	1.00[EUR][1000 genomes]
rs189141	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2116515	1.00[EUR][1000 genomes]
rs2760059	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2981891	1.00[EUR][1000 genomes]
rs2981895	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2987878	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3018408	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs3123641	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332766	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332775	1.00[EUR][1000 genomes]
rs332780	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332785	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332790	1.00[EUR][1000 genomes]
rs332792	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333419	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333425	1.00[EUR][1000 genomes]
rs333434	1.00[EUR][1000 genomes]
rs392368	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4290116	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4309037	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs454643	0.89[AMR][1000 genomes]
rs55659406	1.00[EUR][1000 genomes]
rs56106555	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56357087	1.00[EUR][1000 genomes]
rs58238388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59073370	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60283543	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6672781	1.00[EUR][1000 genomes]
rs6696432	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701696	1.00[EUR][1000 genomes]
rs74126848	1.00[EUR][1000 genomes]
rs74126851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74128516	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv1824383	chr1:174764839-174801748	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1844306	chr1:174764839-174801748	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1819206	chr1:174764839-174802731	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1844208	chr1:174764839-174818547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1847553	chr1:174764839-174818547	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1800291	chr1:174782523-174789611	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1820274	chr1:174782523-174802731	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174769800-174787600	Weak transcription	Pancreas	Pancrea
2	chr1:174770000-174794200	Weak transcription	Fetal Thymus	thymus
3	chr1:174770200-174788200	Weak transcription	Primary T cells from cord blood	blood
4	chr1:174770800-174786400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:174770800-174787600	Weak transcription	Fetal Stomach	stomach
6	chr1:174771600-174787400	Weak transcription	Fetal Brain Male	brain
7	chr1:174772200-174796600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:174777600-174799800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:174781800-174787000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:174782000-174800800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:174782200-174794800	Weak transcription	Fetal Intestine Small	intestine
12	chr1:174782200-174813000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:174782400-174786600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:174782400-174786800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:174782400-174787000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:174782600-174786800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:174782600-174799200	Weak transcription	Liver	Liver
18	chr1:174783000-174786600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:174783600-174789200	Enhancers	NHEK	skin
20	chr1:174783800-174789000	Enhancers	HMEC	breast
21	chr1:174784400-174786600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:174784400-174788000	Weak transcription	Right Atrium	heart
23	chr1:174784400-174789200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:174784400-174797200	Weak transcription	Esophagus	oesophagus
25	chr1:174784800-174806600	Weak transcription	HSMMtube	muscle
26	chr1:174785000-174786400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:174785200-174787200	Enhancers	GM12878-XiMat	blood
28	chr1:174785600-174789200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:174785600-174796000	Weak transcription	Primary B cells from cord blood	blood
30	chr1:174785600-174796800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:174786000-174786200	Enhancers	Left Ventricle	heart
32	chr1:174786000-174787000	Enhancers	Fetal Heart	heart
33	chr1:174786000-174787600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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