Variant report

Variant	rs483877
Chromosome Location	chr6:149658118-149658119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149656360..149658618-chr6:149662826..149665284,3	MCF-7	breast:
2	chr6:149637223..149641886-chr6:149650956..149658366,12	K562	blood:
3	chr6:149638680..149640382-chr6:149658017..149659525,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12110948	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs173140	0.83[EUR][1000 genomes]
rs2031450	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236997	0.89[EUR][1000 genomes]
rs236998	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs236999	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs237000	0.89[EUR][1000 genomes]
rs237004	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs237006	0.83[EUR][1000 genomes]
rs237008	0.82[EUR][1000 genomes]
rs237013	0.89[EUR][1000 genomes]
rs237014	0.89[EUR][1000 genomes]
rs237015	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs237017	0.89[EUR][1000 genomes]
rs237020	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs237022	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs237027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237030	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237031	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237036	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237037	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs365469	0.94[EUR][1000 genomes]
rs389996	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs425278	0.90[JPT][hapmap]
rs425540	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs439495	0.82[CHD][hapmap]
rs473864	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474587	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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]
rs500860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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]
rs520551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520683	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537843	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543711	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[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]
rs548925	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551627	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs558044	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs559848	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs567816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573684	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576022	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs579666	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916134	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926840	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752947	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[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	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv517889	chr6:149653792-149658118	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
2	chr6:149641600-149660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr6:149641800-149660200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:149648400-149660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:149648600-149659200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:149648600-149659600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:149649000-149660200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:149649400-149659000	Enhancers	Primary T cells from cord blood	blood
10	chr6:149649400-149689400	Weak transcription	Fetal Brain Female	brain
11	chr6:149649800-149660200	Weak transcription	Gastric	stomach
12	chr6:149651400-149660000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:149651400-149660000	Enhancers	Liver	Liver
14	chr6:149651600-149659200	Enhancers	Dnd41	blood
15	chr6:149651800-149658400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:149652000-149659000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:149652000-149659400	Enhancers	Brain Anterior Caudate	brain
18	chr6:149652200-149658800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:149652400-149659600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:149652600-149658200	Enhancers	NHDF-Ad	bronchial
21	chr6:149652600-149659000	Enhancers	Osteobl	bone
22	chr6:149652600-149659400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:149652600-149659400	Enhancers	Rectal Smooth Muscle	rectum
24	chr6:149652600-149659600	Enhancers	NH-A	brain
25	chr6:149652600-149659800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:149652800-149660000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:149653200-149660200	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:149654000-149674200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:149654400-149659400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:149654400-149659400	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:149654600-149668600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:149655200-149658200	Enhancers	HSMMtube	muscle
33	chr6:149655200-149658600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:149655200-149659400	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:149655400-149658600	Enhancers	Pancreas	Pancrea
36	chr6:149655400-149659400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:149655400-149660200	Enhancers	Stomach Mucosa	stomach
38	chr6:149655600-149658200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:149655600-149658600	Enhancers	Fetal Thymus	thymus
40	chr6:149655600-149659400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:149655600-149659800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr6:149655800-149659800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:149655800-149659800	Enhancers	Primary B cells from cord blood	blood
44	chr6:149655800-149660200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr6:149656000-149659600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:149656200-149659000	Enhancers	HUVEC	blood vessel
47	chr6:149656200-149659400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:149656200-149659600	Enhancers	Hela-S3	cervix
49	chr6:149656200-149670800	Weak transcription	Esophagus	oesophagus
50	chr6:149656400-149659600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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