Variant report

Variant	rs10186340
Chromosome Location	chr2:100109913-100109914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100046503..100049390-chr2:100109448..100111972,2	MCF-7	breast:
2	chr2:100108007..100111568-chr2:100119889..100123182,3	K562	blood:
3	chr2:100105801..100108163-chr2:100108777..100110702,3	K562	blood:
4	chr2:100106008..100108936-chr2:100109053..100113272,5	MCF-7	breast:
5	chr2:100105579..100107417-chr2:100107751..100110835,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1000409	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1011633	0.81[ASN][1000 genomes]
rs10170425	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10172068	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10172752	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10173466	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10187843	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10205985	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11123786	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11679115	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11683651	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11887109	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11887574	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11902994	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12464535	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12478488	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12621141	0.82[AMR][1000 genomes]
rs12623540	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13018274	0.82[EUR][1000 genomes]
rs13384883	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13389623	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13392042	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13394688	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13427780	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1376443	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1451243	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1807985	0.80[EUR][1000 genomes]
rs1839666	0.83[ASN][1000 genomes]
rs1901283	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1973011	0.83[ASN][1000 genomes]
rs2242037	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290256	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2305354	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2309585	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309586	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2309604	0.81[ASN][1000 genomes]
rs28369943	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28382954	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3087386	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792134	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792146	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792149	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792152	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3811555	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3828316	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4143760	0.81[ASN][1000 genomes]
rs4535093	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850903	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851205	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851208	0.83[ASN][1000 genomes]
rs55867742	0.80[AMR][1000 genomes]
rs62155809	0.81[ASN][1000 genomes]
rs6542879	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542880	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542882	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6706607	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6708861	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6713792	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6714244	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6715321	0.83[ASN][1000 genomes]
rs6717515	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6734290	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6737560	0.81[ASN][1000 genomes]
rs6761390	0.80[ASN][1000 genomes]
rs7558074	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7560795	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7561079	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7564587	0.81[ASN][1000 genomes]
rs7567674	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7571202	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7574135	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7579403	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7580448	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585721	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7586892	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7587419	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7591212	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7598629	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7601470	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7601730	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896249	0.81[ASN][1000 genomes]
rs959929	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806302	chr2:100094799-100123030	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv582524	chr2:100103752-100110353	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10186340	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs10186340	TSGA10	cis	multi-tissue	Pritchard
rs10186340	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs10186340	REV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100107400-100110400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:100107400-100111600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:100107600-100110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:100107600-100111600	Weak transcription	Fetal Kidney	kidney
5	chr2:100107600-100111600	Weak transcription	Fetal Lung	lung
6	chr2:100107600-100111800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:100107600-100111800	Weak transcription	A549	lung
8	chr2:100107600-100112400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:100107600-100112400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:100107600-100113000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:100107600-100119600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:100107800-100111600	Weak transcription	K562	blood
13	chr2:100109400-100112000	Weak transcription	HepG2	liver

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