Variant report

Variant	rs2221416
Chromosome Location	chr2:98885925-98885926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98316350..98317297-chr2:98885417..98886570,3	MCF-7	breast:
2	chr2:98422785..98423811-chr2:98885571..98886436,3	MCF-7	breast:
3	chr2:98424321..98425194-chr2:98885366..98886224,2	K562	blood:
4	chr2:98885600..98886159-chr2:99001199..99001715,2	MCF-7	breast:
5	chr2:98326087..98326680-chr2:98885400..98886287,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10172087	0.80[ASN][1000 genomes]
rs10176056	0.98[ASN][1000 genomes]
rs10181000	0.87[CHB][hapmap];0.81[AFR][1000 genomes]
rs10190336	0.86[ASN][1000 genomes]
rs10199476	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs10201994	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10202618	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124096	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.80[ASN][1000 genomes]
rs11124107	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11124119	0.80[ASN][1000 genomes]
rs11124121	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11673807	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap]
rs11679920	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs11889349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11891512	0.84[ASN][1000 genomes]
rs11895654	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs11901562	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12470615	0.91[LWK][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap]
rs12478763	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12478769	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12622324	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12624294	0.98[ASN][1000 genomes]
rs12712256	0.94[ASN][1000 genomes]
rs12993718	0.84[ASN][1000 genomes]
rs12993818	0.80[ASN][1000 genomes]
rs12999985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs13013876	0.84[ASN][1000 genomes]
rs13014142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs13033263	0.84[ASN][1000 genomes]
rs13394706	0.87[CHB][hapmap]
rs13408372	0.85[CHB][hapmap]
rs13415414	0.98[ASN][1000 genomes]
rs13428221	0.81[ASN][1000 genomes]
rs1451251	1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1466944	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1504679	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17427684	1.00[ASN][1000 genomes]
rs17428056	0.98[ASN][1000 genomes]
rs17429208	0.87[ASW][hapmap];0.87[CHB][hapmap]
rs17493655	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17493788	0.98[ASN][1000 genomes]
rs1875880	1.00[ASN][1000 genomes]
rs2102270	0.87[CHB][hapmap]
rs2122756	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2202387	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2292118	0.87[CHB][hapmap];0.83[AFR][1000 genomes]
rs2292119	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3731659	0.96[ASN][1000 genomes]
rs4374424	0.93[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs4389366	0.94[ASN][1000 genomes]
rs4455212	1.00[CHB][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs4477970	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs4479470	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4494805	0.84[ASN][1000 genomes]
rs4535095	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4608580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4632400	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4851122	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4851123	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851124	0.96[ASN][1000 genomes]
rs4851935	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap]
rs4851951	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4851952	0.84[ASN][1000 genomes]
rs4851953	0.81[ASN][1000 genomes]
rs4851954	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851959	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851960	0.89[ASN][1000 genomes]
rs62157914	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543419	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs6543459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66464436	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6715989	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6725543	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6742930	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6747344	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6747410	0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs6750975	0.96[ASN][1000 genomes]
rs6754222	0.81[CHB][hapmap];0.81[AFR][1000 genomes]
rs72933220	0.98[ASN][1000 genomes]
rs7572757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574218	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs7589018	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598554	0.94[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs7601503	0.80[ASN][1000 genomes]
rs7606070	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7606220	0.93[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.84[YRI][hapmap]
rs937726	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv582515	chr2:98855497-98885925	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv517669	chr2:98855497-98889961	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv437289	chr2:98855497-98891519	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3459702	chr2:98856083-98886708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3459703	chr2:98856205-98886602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv19987	chr2:98856422-98886491	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1012433	chr2:98858308-98888391	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1012121	chr2:98858308-98889961	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3693390	chr2:98862097-98886666	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv438363	chr2:98872039-98885925	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv963671	chr2:98872606-98886425	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1008152	chr2:98875735-98889961	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1002366	chr2:98877050-98904494	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2221416	ZNF514	cis	parietal	SCAN
rs2221416	MRPS5	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98885400-98887200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:98885600-98886200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:98885600-98886200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:98885600-98886200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:98885600-98886400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:98885600-98886600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:98885600-98892200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:98885800-98886000	Enhancers	Colon Smooth Muscle	Colon
9	chr2:98885800-98886200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:98885800-98886600	Enhancers	Aorta	Aorta

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