Variant report

Variant	rs17454164
Chromosome Location	chr2:179995839-179995840
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179988043..179990926-chr2:179994238..179996343,2	K562	blood:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction
ENSG00000238339	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1048026	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10497534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11892241	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11900884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12105478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866665	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16866673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17363183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17363246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17363323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17363393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17363449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17363603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes]
rs17453976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17454192	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17454458	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1838872	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2008215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2028906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3816345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4101465	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4499457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58582728	1.00[AFR][1000 genomes]
rs60072979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61179885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433759	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433766	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs879539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3397115	chr2:179995594-179995922	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:179972600-180001800	Weak transcription	NHEK	skin
7	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
9	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
10	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
11	chr2:179973400-180012600	Weak transcription	NHLF	lung
12	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
15	chr2:179977400-180004400	Weak transcription	Lung	lung
16	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
17	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
18	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
21	chr2:179980000-180038800	Weak transcription	HMEC	breast
22	chr2:179980000-180056800	Weak transcription	HSMM	muscle
23	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:179981400-180001800	Weak transcription	Placenta	Placenta
26	chr2:179981400-180005000	Weak transcription	Ovary	ovary
27	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:179981600-179997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:179981600-180004400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:179981600-180005000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:179981800-180005400	Weak transcription	Osteobl	bone
32	chr2:179982400-180004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:179982800-180004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:179982800-180004600	Weak transcription	Fetal Brain Male	brain
35	chr2:179983600-180005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:179984600-180003000	Weak transcription	Fetal Lung	lung
37	chr2:179984600-180004600	Weak transcription	HUVEC	blood vessel
38	chr2:179984800-180002000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:179984800-180004200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:179984800-180005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
42	chr2:179985200-180004400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:179985200-180004400	Weak transcription	Fetal Stomach	stomach
44	chr2:179985400-180004000	Weak transcription	Dnd41	blood
45	chr2:179985600-179996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:179985600-180005800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:179985800-180004000	Weak transcription	Fetal Intestine Large	intestine
48	chr2:179985800-180004400	Weak transcription	Fetal Brain Female	brain
49	chr2:179985800-180004400	Weak transcription	Left Ventricle	heart
50	chr2:179985800-180005800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links