Variant report

Variant	rs5744646
Chromosome Location	chr5:74871127-74871128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74868580..74871320-chr5:74902166..74903871,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs57057408	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744586	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744600	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59629012	1.00[AMR][1000 genomes]
rs60835393	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73118895	1.00[AMR][1000 genomes]
rs73118896	1.00[AMR][1000 genomes]
rs73118899	1.00[AMR][1000 genomes]
rs73120827	1.00[AMR][1000 genomes]
rs73120838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73120840	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73120841	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73120845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73122736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73122748	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882201	chr5:74787310-74890618	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74818200-74897400	Weak transcription	Thymus	Thymus
2	chr5:74822800-74896000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr5:74831200-74877200	Weak transcription	Fetal Kidney	kidney
4	chr5:74833400-74906800	Weak transcription	Brain Substantia Nigra	brain
5	chr5:74837600-74874400	Weak transcription	Fetal Brain Male	brain
6	chr5:74839400-74897400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:74841200-74899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:74850000-74878000	Weak transcription	HepG2	liver
9	chr5:74850200-74896200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:74851200-74872600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:74854000-74883400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:74855600-74872600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:74862200-74873400	Weak transcription	Fetal Brain Female	brain
14	chr5:74862200-74897800	Weak transcription	Brain Germinal Matrix	brain
15	chr5:74862600-74887600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:74862600-74888800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:74862600-74897200	Weak transcription	Lung	lung
18	chr5:74862800-74872600	Weak transcription	Placenta	Placenta
19	chr5:74862800-74874800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:74862800-74874800	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:74862800-74888600	Weak transcription	Fetal Intestine Small	intestine
22	chr5:74862800-74888800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:74862800-74897400	Weak transcription	Pancreas	Pancrea
24	chr5:74862800-74897400	Weak transcription	Spleen	Spleen
25	chr5:74862800-74897600	Weak transcription	Gastric	stomach
26	chr5:74862800-74907200	Weak transcription	Esophagus	oesophagus
27	chr5:74863000-74886400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:74863000-74896200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:74863200-74872600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:74863200-74872800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:74863600-74873000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:74863600-74905800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:74863800-74872200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:74863800-74873200	Weak transcription	HSMMtube	muscle
35	chr5:74863800-74883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:74863800-74906800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:74864000-74872800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:74864000-74874400	Weak transcription	Right Ventricle	heart
39	chr5:74864000-74875000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:74864000-74877800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:74864000-74884200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:74864000-74889000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:74864000-74897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:74864000-74897400	Weak transcription	NHEK	skin
45	chr5:74864000-74899600	Weak transcription	Hela-S3	cervix
46	chr5:74864000-74907000	Weak transcription	Psoas Muscle	Psoas
47	chr5:74864200-74872400	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:74864200-74880400	Weak transcription	Stomach Mucosa	stomach
49	chr5:74864200-74884600	Weak transcription	Fetal Heart	heart
50	chr5:74864200-74886400	Weak transcription	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