Variant report

Variant	rs559204
Chromosome Location	chr6:149660498-149660499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:149660288-149660499	ProgFib	skin:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149659981..149662112-chr6:149664199..149665904,2	MCF-7	breast:
2	chr6:149649733..149652455-chr6:149658613..149661110,2	K562	blood:
3	chr6:149654628..149657508-chr6:149659280..149661788,2	MCF-7	breast:
4	chr6:149652416..149655199-chr6:149659324..149661368,2	K562	blood:
5	chr6:149636719..149639500-chr6:149659971..149661713,2	MCF-7	breast:
6	chr6:149658537..149661655-chr6:149675884..149678661,3	MCF-7	breast:

No data

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs17086451	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2341783	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341784	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744427	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744428	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744431	0.80[EUR][1000 genomes]
rs2744433	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2744434	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789487	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789489	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789490	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789500	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734296	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4360154	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs472620	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474369	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs478531	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs478767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480526	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480778	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs481769	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897117	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs490529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs492956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs504762	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511105	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs513923	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs515133	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs527971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs532008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532250	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs533026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538386	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554926	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556335	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs559052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565825	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588028	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60006373	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs600739	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630642	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs641068	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs652514	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs652921	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs663625	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs674919	0.80[EUR][1000 genomes]
rs681919	0.84[EUR][1000 genomes]
rs92605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9373591	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377216	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377217	0.80[EUR][1000 genomes]
rs9390676	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399686	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404032	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404034	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9404035	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404037	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:111 , 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	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:149648400-149660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:149649400-149689400	Weak transcription	Fetal Brain Female	brain
5	chr6:149654000-149674200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:149654600-149668600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:149656200-149670800	Weak transcription	Esophagus	oesophagus
8	chr6:149656800-149661800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:149656800-149681400	Weak transcription	Psoas Muscle	Psoas
10	chr6:149656800-149682400	Weak transcription	Lung	lung
11	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
12	chr6:149657400-149663600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:149657400-149665800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:149657600-149663200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:149657800-149661400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:149657800-149673800	Weak transcription	Thymus	Thymus
17	chr6:149657800-149683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:149657800-149691200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:149658000-149661200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:149658000-149661400	Weak transcription	HSMM	muscle
21	chr6:149658000-149662800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:149658000-149663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:149658000-149663200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:149658000-149663400	Weak transcription	Small Intestine	intestine
25	chr6:149658000-149663800	Weak transcription	Aorta	Aorta
26	chr6:149658000-149663800	Weak transcription	Right Ventricle	heart
27	chr6:149658000-149673800	Weak transcription	Fetal Intestine Large	intestine
28	chr6:149658000-149673800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:149658000-149674000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:149658000-149679000	Weak transcription	K562	blood
31	chr6:149658000-149680800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:149658000-149681400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:149658000-149695400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:149658200-149662400	Weak transcription	HSMMtube	muscle
35	chr6:149658200-149664800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:149658200-149691000	Weak transcription	NHDF-Ad	bronchial
37	chr6:149658600-149661200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:149658600-149664400	Weak transcription	Right Atrium	heart
39	chr6:149658800-149663600	Weak transcription	NHEK	skin
40	chr6:149658800-149666400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:149658800-149674000	Weak transcription	HepG2	liver
42	chr6:149658800-149692400	Weak transcription	Fetal Kidney	kidney
43	chr6:149659000-149660600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:149659000-149661000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:149659000-149661000	Weak transcription	Osteobl	bone
46	chr6:149659000-149661200	Weak transcription	Primary T cells from cord blood	blood
47	chr6:149659000-149661400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:149659000-149662600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:149659000-149664800	Weak transcription	HUVEC	blood vessel
50	chr6:149659200-149661200	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links