Variant report

Variant	rs7659164
Chromosome Location	chr4:48129801-48129802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48127393..48130014-chr4:48270047..48272078,2	MCF-7	breast:
2	chr4:48129577..48130360-chr4:48317760..48318680,2	K562	blood:
3	chr4:48129508..48130326-chr4:48548279..48548799,3	K562	blood:
4	chr4:48111525..48112261-chr4:48129446..48130015,2	MCF-7	breast:
5	chr4:48129433..48130199-chr4:48276992..48278818,4	MCF-7	breast:
6	chr4:48129477..48130456-chr4:48142756..48143626,3	K562	blood:
7	chr4:48129602..48130429-chr4:48277151..48277985,3	MCF-7	breast:
8	chr4:48123791..48126043-chr4:48128232..48130518,2	MCF-7	breast:
9	chr4:48129523..48130363-chr4:48143099..48143691,2	MCF-7	breast:
10	chr4:48129338..48130462-chr4:48292123..48292901,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10027991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938524	0.85[ASN][1000 genomes]
rs11944549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512766	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507919	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860999	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2089510	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2243840	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2464502	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661529	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661533	0.82[EUR][1000 genomes]
rs2661543	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661544	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661547	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661548	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704399	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704426	1.00[ASN][1000 genomes]
rs2704433	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704435	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704436	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704439	0.83[EUR][1000 genomes]
rs3805184	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695341	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447616	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814443	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819592	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7678246	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689953	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882715	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7659164	TXK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48123000-48137600	Weak transcription	Gastric	stomach
2	chr4:48126600-48133400	Enhancers	K562	blood
3	chr4:48128800-48130400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr4:48128800-48130400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:48128800-48132000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:48129000-48130400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:48129000-48130400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:48129000-48132400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:48129200-48130000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:48129200-48130000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:48129200-48130000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:48129200-48130000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr4:48129200-48130000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:48129200-48130000	Enhancers	HMEC	breast
15	chr4:48129200-48130200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr4:48129200-48130200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:48129200-48130400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:48129200-48130400	Enhancers	Fetal Intestine Large	intestine
19	chr4:48129200-48130400	Enhancers	Fetal Muscle Leg	muscle
20	chr4:48129200-48130400	Enhancers	Small Intestine	intestine
21	chr4:48129200-48130600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:48129200-48130600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:48129200-48130800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:48129200-48131800	Enhancers	NHLF	lung
25	chr4:48129200-48132000	Enhancers	GM12878-XiMat	blood
26	chr4:48129200-48136600	Enhancers	Fetal Heart	heart
27	chr4:48129400-48130000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
28	chr4:48129400-48130000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr4:48129400-48130200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr4:48129400-48130400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr4:48129400-48130400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr4:48129400-48130400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr4:48129400-48130400	Enhancers	Fetal Intestine Small	intestine
34	chr4:48129400-48130400	Enhancers	Right Atrium	heart
35	chr4:48129400-48130400	Enhancers	Stomach Mucosa	stomach
36	chr4:48129400-48130400	Flanking Active TSS	HSMMtube	muscle
37	chr4:48129400-48130600	Enhancers	Primary B cells from peripheral blood	blood
38	chr4:48129400-48130600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr4:48129400-48130600	Enhancers	Liver	Liver
40	chr4:48129400-48131600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr4:48129400-48132200	Enhancers	Primary hematopoietic stem cells	blood
42	chr4:48129400-48135000	Enhancers	Fetal Thymus	thymus
43	chr4:48129600-48130000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:48129600-48130000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:48129600-48130000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr4:48129600-48130000	Enhancers	Right Ventricle	heart
47	chr4:48129600-48130000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:48129600-48130200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:48129600-48130200	Enhancers	Primary B cells from cord blood	blood
50	chr4:48129600-48130200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links