Variant report

Variant	rs28594421
Chromosome Location	chr3:196105530-196105531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196068341..196070140-chr3:196103997..196105996,2	K562	blood:
2	chr16:4526518..4527018-chr3:196105176..196106110,2	Hela-S3	cervix:
3	chr3:196100863..196102886-chr3:196104953..196107824,2	K562	blood:
4	chr3:196105489..196108118-chr3:196158245..196159887,2	K562	blood:
5	chr3:196082786..196084375-chr3:196104445..196107093,2	K562	blood:
6	chr3:196090966..196093753-chr3:196102999..196105784,2	K562	blood:

Variant related genes	Relation type
ENSG00000163960	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000212146	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10881567	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11185537	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712853	0.85[EUR][1000 genomes]
rs12488531	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12638961	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073879	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13089205	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28549737	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34702811	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35561509	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4133244	0.83[AMR][1000 genomes]
rs4290832	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4371545	0.85[EUR][1000 genomes]
rs4513483	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4579046	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4916428	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6583303	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6774540	0.84[EUR][1000 genomes]
rs73213970	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7373049	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7373103	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7373385	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7374841	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7617626	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7624107	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9821735	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9839978	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9841810	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9847223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9848247	0.85[EUR][1000 genomes]
rs9860931	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9874783	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196070600-196106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
4	chr3:196083800-196106400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:196084600-196131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:196086400-196116000	Weak transcription	A549	lung
7	chr3:196088400-196116600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:196089000-196106600	Weak transcription	Right Ventricle	heart
9	chr3:196089400-196107000	Weak transcription	Aorta	Aorta
10	chr3:196089400-196116400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:196089600-196106400	Weak transcription	HSMMtube	muscle
12	chr3:196089600-196113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:196089600-196115600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
15	chr3:196089800-196109200	Weak transcription	Fetal Brain Male	brain
16	chr3:196089800-196115800	Weak transcription	HUVEC	blood vessel
17	chr3:196089800-196116200	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:196090800-196106400	Weak transcription	NHLF	lung
19	chr3:196094000-196116400	Weak transcription	Gastric	stomach
20	chr3:196094000-196126200	Weak transcription	Colonic Mucosa	Colon
21	chr3:196094200-196116400	Weak transcription	Esophagus	oesophagus
22	chr3:196094800-196106200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:196094800-196115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:196094800-196115800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:196094800-196115800	Weak transcription	Brain Angular Gyrus	brain
26	chr3:196095000-196106200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:196095000-196106200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:196095000-196106400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:196095000-196106400	Weak transcription	Fetal Brain Female	brain
30	chr3:196095000-196107000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:196095000-196115400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:196095000-196115400	Weak transcription	NH-A	brain
33	chr3:196095600-196106000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
35	chr3:196096400-196115400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:196096600-196106400	Weak transcription	Primary B cells from cord blood	blood
37	chr3:196096800-196106200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:196098000-196126800	Weak transcription	Pancreas	Pancrea
39	chr3:196098200-196106000	Weak transcription	Fetal Lung	lung
40	chr3:196098200-196106200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:196098200-196106200	Weak transcription	Fetal Kidney	kidney
42	chr3:196098200-196106400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:196098200-196116000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:196098200-196116000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:196098400-196106200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:196098400-196106400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:196098400-196106400	Weak transcription	Adipose Nuclei	Adipose
48	chr3:196098400-196106400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:196098400-196117000	Weak transcription	Brain Substantia Nigra	brain
50	chr3:196098600-196106200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links