Variant report

Variant	rs1890612
Chromosome Location	chr6:149414461-149414462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149401028..149403801-chr6:149413849..149415930,2	MCF-7	breast:
2	chr6:149413026..149415707-chr6:149636952..149639609,2	MCF-7	breast:
3	chr6:149414073..149415893-chr6:149615671..149617691,2	MCF-7	breast:
4	chr6:149412611..149415289-chr6:149531964..149533952,2	MCF-7	breast:
5	chr6:149414327..149416507-chr6:149637915..149640707,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10457075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10457839	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10457842	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10499251	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12153925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12196284	1.00[JPT][hapmap]
rs12197040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12200909	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12202158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12206419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12216011	0.85[EUR][1000 genomes]
rs1316376	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316534	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1316536	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13190879	0.84[EUR][1000 genomes]
rs13217006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17669546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1890610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1934222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1934223	0.82[EUR][1000 genomes]
rs2153251	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2153252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2185250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340800	0.85[EUR][1000 genomes]
rs34118116	0.82[EUR][1000 genomes]
rs34599887	0.82[EUR][1000 genomes]
rs3949414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4313020	0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs4332004	0.83[EUR][1000 genomes]
rs4336467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4441968	0.83[EUR][1000 genomes]
rs4454159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6570924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6570926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6570927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6570932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570939	0.85[EUR][1000 genomes]
rs6900527	1.00[JPT][hapmap]
rs6901626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902195	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902487	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909527	1.00[JPT][hapmap]
rs6909624	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6914318	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6917010	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6924503	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6930713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6932773	0.82[EUR][1000 genomes]
rs6940664	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6940915	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7762928	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775412	0.85[EUR][1000 genomes]
rs7776204	1.00[JPT][hapmap]
rs9322165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9485353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9498197	0.83[EUR][1000 genomes]
rs9498199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9498201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9498202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9498204	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9498205	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498214	0.86[EUR][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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149395000-149415000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:149399200-149415000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:149402200-149414600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:149402200-149415000	Weak transcription	Esophagus	oesophagus
5	chr6:149402400-149416200	Weak transcription	Fetal Heart	heart
6	chr6:149409800-149415000	Weak transcription	Gastric	stomach
7	chr6:149410000-149415000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:149410200-149414800	Weak transcription	Placenta	Placenta
9	chr6:149410600-149415000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:149410800-149418400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:149411800-149414800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:149411800-149415800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:149412200-149415200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:149412400-149414600	Weak transcription	Fetal Stomach	stomach
15	chr6:149413000-149415600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:149413000-149415600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:149413000-149416000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:149413000-149416000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:149413000-149416000	Enhancers	Dnd41	blood
20	chr6:149413200-149415200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:149413200-149416000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:149413400-149416000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:149413600-149416000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:149414000-149415200	Weak transcription	GM12878-XiMat	blood
25	chr6:149414000-149415800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:149414200-149417600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:149414200-149418400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:149414400-149414600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:149414400-149414600	Enhancers	Fetal Kidney	kidney
30	chr6:149414400-149415200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:149414400-149415600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr6:149414400-149415600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:149414400-149415600	Enhancers	NHLF	lung
34	chr6:149414400-149416200	Enhancers	Fetal Lung	lung
35	chr6:149414400-149416400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:149414400-149416400	Enhancers	NH-A	brain

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