Variant report

Variant	rs1316534
Chromosome Location	chr6:149417543-149417544
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	chr6:149411028..149414367-chr6:149415075..149417889,3	MCF-7	breast:
2	chr6:149405339..149407233-chr6:149416159..149418196,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10457075	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10457839	1.00[JPT][hapmap]
rs10457842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10499251	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12153925	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12196284	1.00[JPT][hapmap]
rs12197040	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12200909	1.00[JPT][hapmap]
rs12202158	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12206419	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12216011	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1316376	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1316536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191650	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217006	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17669546	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1890610	0.86[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1890612	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1934221	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1934222	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2153251	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2153252	0.85[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs2185250	0.86[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2340800	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3949414	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4336467	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4454159	0.86[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6570923	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570924	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570926	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6570927	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6570932	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6570939	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6900527	1.00[JPT][hapmap]
rs6901626	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6902195	0.84[EUR][1000 genomes]
rs6902487	0.84[EUR][1000 genomes]
rs6909527	1.00[JPT][hapmap]
rs6909624	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6914281	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6914318	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6914925	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6917010	0.86[ASW][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6924503	0.84[EUR][1000 genomes]
rs6930713	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6940664	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6940915	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7740618	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7762928	0.86[ASW][hapmap];0.85[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs7773409	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7775412	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7776204	1.00[JPT][hapmap]
rs9322165	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9485353	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9498199	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498201	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9498202	0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9498204	0.93[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9498205	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9498207	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9498214	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149410800-149418400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:149414200-149417600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr6:149414200-149418400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:149414600-149417600	Enhancers	Primary T cells from cord blood	blood
5	chr6:149414800-149418000	Enhancers	Primary hematopoietic stem cells	blood
6	chr6:149415200-149418200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:149415200-149419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:149415400-149418400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:149415600-149418000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:149415800-149417800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:149416000-149417600	Flanking Active TSS	Dnd41	blood
12	chr6:149416200-149418800	Weak transcription	Fetal Lung	lung
13	chr6:149416400-149417800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:149416400-149417800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:149416400-149417800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:149416400-149418000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:149416400-149418000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:149416400-149418800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:149416400-149418800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:149416400-149418800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:149416600-149418200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:149416800-149418400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr6:149417000-149417600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:149417000-149418000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:149417200-149418000	Enhancers	Brain Hippocampus Middle	brain
26	chr6:149417400-149417600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:149417400-149417600	Enhancers	Small Intestine	intestine

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