Variant report

Variant	rs6805727
Chromosome Location	chr3:45979023-45979024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:45978920-45979070	GM12864	blood:	n/a	n/a
2	CTCF	chr3:45978900-45979050	HBMEC	blood vessel:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:45979007..45979682-chr3:46117842..46118764,2	MCF-7	breast:
2	chr3:45978817..45979385-chr3:46120279..46120902,2	K562	blood:
3	chr3:45978760..45981889-chr3:46119716..46121321,25	MCF-7	breast:
4	chr3:45969350..45971618-chr3:45977990..45979825,2	MCF-7	breast:
5	chr3:45976449..45979237-chr3:45991973..45993587,2	K562	blood:
6	chr3:45972956..45974535-chr3:45977959..45979517,2	K562	blood:
7	chr3:45973841..45976554-chr3:45977102..45979618,2	MCF-7	breast:
8	chr3:45978904..45980774-chr3:45983050..45984937,2	MCF-7	breast:
9	chr3:45978672..45979831-chr3:46120014..46120974,3	MCF-7	breast:

No data

Variant related genes	Relation type
CXCR6	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12330199	0.85[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6806348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7618618	1.00[YRI][hapmap]
rs9814852	0.84[AFR][1000 genomes]
rs9825221	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9825682	0.97[AFR][1000 genomes]
rs9825804	0.97[AFR][1000 genomes]
rs9833683	0.91[AFR][1000 genomes]
rs9840179	0.93[AFR][1000 genomes]
rs9860832	0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9865446	0.90[AFR][1000 genomes]
rs9875356	0.85[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9880627	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
5	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:45959800-45979800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:45959800-45979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:45960000-45979400	Strong transcription	Fetal Intestine Large	intestine
12	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:45960400-45980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:45961600-45979400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:45961600-45979800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:45963800-45979800	Strong transcription	Primary T cells from cord blood	blood
18	chr3:45963800-45979800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:45964400-45980400	Weak transcription	Fetal Brain Female	brain
20	chr3:45965400-45980400	Weak transcription	Fetal Brain Male	brain
21	chr3:45966000-45980600	Weak transcription	HMEC	breast
22	chr3:45966800-45979600	Strong transcription	Liver	Liver
23	chr3:45967200-45979400	Strong transcription	Adipose Nuclei	Adipose
24	chr3:45967200-45979800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:45967200-45980000	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:45967400-45979800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:45968000-45979200	Strong transcription	Placenta	Placenta
28	chr3:45968400-45979800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:45968400-45979800	Strong transcription	Ovary	ovary
30	chr3:45968600-45979800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr3:45968600-45980200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr3:45968800-45979200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:45968800-45979200	Strong transcription	HepG2	liver
34	chr3:45968800-45979400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:45968800-45979400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:45968800-45979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:45969000-45979200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:45969000-45979200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:45969000-45979600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:45969200-45979800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:45969200-45979800	Strong transcription	Colon Smooth Muscle	Colon
42	chr3:45970000-45980400	Weak transcription	Right Atrium	heart
43	chr3:45970200-45980400	Weak transcription	NH-A	brain
44	chr3:45970200-45980600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:45971000-45979400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:45971000-45979800	Strong transcription	Thymus	Thymus
48	chr3:45971000-45980200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:45971400-45980200	Strong transcription	Dnd41	blood
50	chr3:45971800-45982400	Weak transcription	NHEK	skin

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