Variant report

Variant	rs10001246
Chromosome Location	chr4:79527272-79527273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79527063..79529896-chr4:79532184..79534959,3	K562	blood:
2	chr4:79526850..79529113-chr4:79529739..79531752,2	K562	blood:
3	chr4:79527192..79529448-chr4:79696631..79698650,2	K562	blood:

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10212636	0.84[EUR][1000 genomes]
rs1107606	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1108907	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11724268	0.90[CEU][hapmap]
rs11724602	0.84[EUR][1000 genomes]
rs11733032	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs11733269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736376	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs11736602	0.90[CEU][hapmap]
rs11942573	0.81[CEU][hapmap]
rs12233694	0.90[CEU][hapmap]
rs12643488	0.84[EUR][1000 genomes]
rs12646646	0.82[EUR][1000 genomes]
rs12711032	0.82[CEU][hapmap]
rs13110339	0.81[CEU][hapmap]
rs13120630	0.81[CEU][hapmap]
rs13138005	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1587222	0.85[JPT][hapmap]
rs1972024	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4306980	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4353930	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4975148	0.83[EUR][1000 genomes]
rs6533821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533825	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533835	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6533842	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6533847	0.91[CEU][hapmap]
rs6811335	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6824014	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6829061	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6829198	0.84[EUR][1000 genomes]
rs6834587	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6835210	0.95[CEU][hapmap]
rs6835998	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6838443	0.82[CEU][hapmap]
rs6840592	0.91[CEU][hapmap]
rs6841654	0.91[CEU][hapmap]
rs6845893	0.81[CEU][hapmap]
rs6846346	0.84[EUR][1000 genomes]
rs6854055	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7317	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7657082	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7677783	0.81[CEU][hapmap]
rs7680749	0.84[EUR][1000 genomes]
rs7680766	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7689154	0.84[EUR][1000 genomes]
rs9998136	0.83[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv967949	chr4:79511515-79527707	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:79488400-79527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
5	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:79491800-79542600	Weak transcription	NH-A	brain
8	chr4:79492000-79531600	Strong transcription	HMEC	breast
9	chr4:79502200-79529200	Weak transcription	Colonic Mucosa	Colon
10	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:79508800-79527400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:79513800-79534200	Strong transcription	NHEK	skin
16	chr4:79517200-79534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:79518400-79528200	Strong transcription	Fetal Intestine Large	intestine
19	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
20	chr4:79519200-79528400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:79521200-79527600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:79521400-79529800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:79521400-79534000	Weak transcription	Right Ventricle	heart
24	chr4:79522200-79529600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:79522600-79531200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:79522600-79531600	Weak transcription	HSMMtube	muscle
27	chr4:79523600-79533800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:79523800-79528800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr4:79524000-79528200	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:79524200-79528800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:79524200-79529000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:79524200-79529800	Weak transcription	Fetal Heart	heart
33	chr4:79524200-79543400	Weak transcription	A549	lung
34	chr4:79524400-79530400	Weak transcription	Hela-S3	cervix
35	chr4:79524400-79532000	Weak transcription	Pancreas	Pancrea
36	chr4:79524400-79534000	Weak transcription	Placenta	Placenta
37	chr4:79524800-79530000	Weak transcription	Primary T cells from cord blood	blood
38	chr4:79525000-79529600	Weak transcription	K562	blood
39	chr4:79525000-79529800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:79525200-79528200	Strong transcription	HUVEC	blood vessel
41	chr4:79525600-79531600	Weak transcription	Thymus	Thymus
42	chr4:79525800-79527800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:79526200-79527800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:79526400-79528000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:79526600-79527800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:79526800-79527600	Strong transcription	Gastric	stomach
47	chr4:79526800-79527800	Strong transcription	Fetal Stomach	stomach
48	chr4:79526800-79528000	Strong transcription	Fetal Intestine Small	intestine
49	chr4:79526800-79528000	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr4:79527000-79527400	Strong transcription	Lung	lung

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