Variant report

Variant	rs7579999
Chromosome Location	chr2:99857670-99857671
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	chr2:99855888..99858243-chr2:99952048..99955134,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10179435	0.80[EUR][1000 genomes]
rs10180138	0.80[EUR][1000 genomes]
rs10180688	0.89[CEU][hapmap]
rs10186223	0.80[EUR][1000 genomes]
rs10187854	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10207435	0.80[EUR][1000 genomes]
rs10210257	0.80[EUR][1000 genomes]
rs10210346	0.80[EUR][1000 genomes]
rs10496337	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs10865030	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11123769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123776	0.89[EUR][1000 genomes]
rs11123778	0.87[EUR][1000 genomes]
rs11123783	0.80[EUR][1000 genomes]
rs11123784	0.89[CEU][hapmap]
rs11525712	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12162367	0.80[EUR][1000 genomes]
rs12328219	1.00[ASN][1000 genomes]
rs12617324	0.82[EUR][1000 genomes]
rs12623835	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs12992356	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12993310	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	0.80[EUR][1000 genomes]
rs13022798	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13028722	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs13032885	0.87[EUR][1000 genomes]
rs13384665	0.80[ASN][1000 genomes]
rs13393060	1.00[ASN][1000 genomes]
rs13401163	0.89[CEU][hapmap]
rs13404012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13409359	0.89[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs13419448	0.80[EUR][1000 genomes]
rs13426758	0.89[CEU][hapmap]
rs13429185	0.89[CEU][hapmap]
rs13429806	0.80[EUR][1000 genomes]
rs13430662	0.80[ASN][1000 genomes]
rs13432046	0.80[EUR][1000 genomes]
rs1487271	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487272	0.99[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843807	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882598	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs1922625	0.89[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1922627	0.91[EUR][1000 genomes]
rs1948101	0.91[EUR][1000 genomes]
rs2091798	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309577	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2309615	0.89[EUR][1000 genomes]
rs2309616	0.91[EUR][1000 genomes]
rs28745279	0.80[ASN][1000 genomes]
rs3087399	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs35996174	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3828162	0.89[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs4522654	0.89[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4850896	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4850902	0.80[EUR][1000 genomes]
rs4851189	0.90[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4851191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851194	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851197	0.87[EUR][1000 genomes]
rs4851199	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs4851201	0.81[EUR][1000 genomes]
rs6542871	0.90[EUR][1000 genomes]
rs6542877	0.89[EUR][1000 genomes]
rs6706425	0.80[EUR][1000 genomes]
rs6712137	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6721031	0.80[EUR][1000 genomes]
rs6726711	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6728723	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6744199	0.86[EUR][1000 genomes]
rs6745645	0.85[EUR][1000 genomes]
rs6747601	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6749029	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7567230	0.89[EUR][1000 genomes]
rs7567462	0.91[EUR][1000 genomes]
rs7569805	0.89[CEU][hapmap]
rs7579143	0.89[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs7579171	0.87[EUR][1000 genomes]
rs7581337	0.89[EUR][1000 genomes]
rs7582085	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7582133	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7584022	0.83[EUR][1000 genomes]
rs7584705	0.89[EUR][1000 genomes]
rs7586635	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7599384	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7599843	0.91[EUR][1000 genomes]
rs7602401	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602637	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603388	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7606279	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9308819	0.89[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs9308821	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv1001784	chr2:99838079-99910328	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv535840	chr2:99838079-99910328	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv997436	chr2:99840131-99916886	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	esv2762746	chr2:99840143-99916898	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	nsv1001736	chr2:99846306-99916886	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv1009459	chr2:99846306-99918895	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
19	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
20	esv2751904	chr2:99847882-99913998	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv1001235	chr2:99847890-99913998	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
22	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
24	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
25	nsv1007249	chr2:99855978-99916886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
26	nsv1004291	chr2:99855978-99919999	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
27	nsv1010419	chr2:99857259-99897312	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7579999	LIPT1	cis	cerebellum	SCAN
rs7579999	LYG1	cis	Whole Blood	GTEx
rs7579999	TSGA10	cis	cerebellum	SCAN
rs7579999	TSGA10	cis	Thyroid	GTEx
rs7579999	LIPT1	cis	multi-tissue	Pritchard
rs7579999	LIPT1	cis	parietal	SCAN
rs7579999	TSGA10	cis	multi-tissue	Pritchard
rs7579999	LYG1	cis	parietal	SCAN
rs7579999	ARID5A	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99840800-99874400	Weak transcription	Aorta	Aorta
2	chr2:99853600-99863200	Weak transcription	Esophagus	oesophagus
3	chr2:99854800-99865800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links