Variant report

Variant	rs149599
Chromosome Location	chr5:61704664-61704665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61698432..61700828-chr5:61704571..61706391,2	MCF-7	breast:
2	chr5:61698481..61701475-chr5:61702171..61705225,3	K562	blood:
3	chr5:61697532..61701694-chr5:61703408..61710603,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086200	Chromatin interaction
ENSG00000086189	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10054305	0.96[CEU][hapmap]
rs10058044	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs10065749	0.96[CEU][hapmap]
rs10069745	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10461472	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10471545	0.84[CEU][hapmap]
rs10471546	0.80[EUR][1000 genomes]
rs10939937	0.83[EUR][1000 genomes]
rs12515967	0.81[EUR][1000 genomes]
rs12516160	0.84[CEU][hapmap]
rs12696990	0.80[EUR][1000 genomes]
rs1301063	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1309156	0.85[EUR][1000 genomes]
rs13174978	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs13361143	0.96[CEU][hapmap]
rs149540	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs152184	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs152187	0.88[CEU][hapmap]
rs152191	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs152192	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs152199	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs152202	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs152203	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs152208	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152209	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152215	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs153857	0.88[CEU][hapmap]
rs153858	0.88[CEU][hapmap]
rs153862	0.88[CEU][hapmap]
rs1562244	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs166005	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16890622	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs173522	0.88[CEU][hapmap]
rs173523	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs174647	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs181912	0.84[CEU][hapmap]
rs2034240	0.81[EUR][1000 genomes]
rs2289883	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2344396	0.84[CEU][hapmap]
rs247218	0.84[EUR][1000 genomes]
rs247220	0.84[EUR][1000 genomes]
rs247221	0.85[EUR][1000 genomes]
rs247222	0.85[EUR][1000 genomes]
rs247223	0.85[EUR][1000 genomes]
rs247229	0.88[CEU][hapmap]
rs247233	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs247240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247244	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247245	0.88[CEU][hapmap]
rs247247	0.85[CEU][hapmap]
rs247248	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247249	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247255	0.85[EUR][1000 genomes]
rs247265	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs247267	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247268	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247269	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247270	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs247273	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247275	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247494	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs264519	0.81[EUR][1000 genomes]
rs264520	0.81[EUR][1000 genomes]
rs264521	0.81[EUR][1000 genomes]
rs264523	0.81[EUR][1000 genomes]
rs264528	0.81[EUR][1000 genomes]
rs264530	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs264531	0.80[EUR][1000 genomes]
rs26624	0.88[CEU][hapmap]
rs26625	0.85[CEU][hapmap]
rs26628	0.85[CEU][hapmap]
rs26629	0.84[CEU][hapmap]
rs26630	0.88[CEU][hapmap]
rs26631	0.84[ASN][1000 genomes]
rs26632	0.84[ASN][1000 genomes]
rs26637	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26641	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26644	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26645	0.88[CEU][hapmap]
rs27542	0.88[CEU][hapmap]
rs27693	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28539215	0.80[ASN][1000 genomes]
rs28581963	0.80[ASN][1000 genomes]
rs32052	0.96[YRI][hapmap]
rs32154	0.84[CEU][hapmap]
rs32155	0.84[CEU][hapmap]
rs32164	0.84[CEU][hapmap]
rs32171	0.80[CEU][hapmap]
rs32181	0.84[CEU][hapmap]
rs32187	0.84[CEU][hapmap]
rs32188	0.81[CEU][hapmap]
rs35010	0.88[CEU][hapmap]
rs35059	0.88[CEU][hapmap]
rs366238	0.81[CEU][hapmap]
rs3776615	0.83[EUR][1000 genomes]
rs3776638	0.96[CEU][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs3822485	0.96[CEU][hapmap]
rs39923	0.84[CEU][hapmap]
rs39935	0.84[CEU][hapmap]
rs40110	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs438143	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4441833	0.96[CEU][hapmap]
rs4700004	0.85[CEU][hapmap]
rs4700006	0.88[CEU][hapmap]
rs4700009	0.81[EUR][1000 genomes]
rs6881888	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs7700569	0.81[EUR][1000 genomes]
rs7702634	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7717128	0.96[CEU][hapmap]
rs7722692	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7737525	0.96[CEU][hapmap];0.81[ASN][1000 genomes]
rs784921	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9291756	0.85[CEU][hapmap]
rs9291758	0.81[EUR][1000 genomes]
rs959899	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][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	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61700600-61707800	Weak transcription	Right Ventricle	heart
2	chr5:61700800-61707600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:61700800-61707600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr5:61700800-61707600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:61700800-61707600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:61700800-61707600	Weak transcription	Fetal Heart	heart
7	chr5:61700800-61707600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:61700800-61707600	Weak transcription	HUVEC	blood vessel
9	chr5:61700800-61707600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:61700800-61707800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:61700800-61707800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:61700800-61707800	Weak transcription	Placenta	Placenta
13	chr5:61700800-61707800	Weak transcription	Stomach Mucosa	stomach
14	chr5:61701000-61707600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:61701000-61707600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:61701000-61707600	Weak transcription	Liver	Liver
17	chr5:61701000-61707600	Weak transcription	Dnd41	blood
18	chr5:61701000-61707800	Weak transcription	Primary T cells from cord blood	blood
19	chr5:61701000-61707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:61701000-61707800	Weak transcription	Hela-S3	cervix
21	chr5:61701000-61708000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:61701200-61707800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:61701200-61707800	Weak transcription	NHEK	skin

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