Variant report

Variant	rs11743717
Chromosome Location	chr5:74659587-74659588
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	chr5:74653986..74657111-chr5:74658520..74660531,3	K562	blood:
2	chr5:74649780..74652799-chr5:74656910..74662122,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGCR-1	chr5:74659585-74660067	ENSG00000271815.1

Variant related genes	Relation type
ENSG00000113161	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10515198	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742194	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746245	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749414	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17238330	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17244848	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17244855	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17648288	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761738	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761740	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5909	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74635600-74659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:74637200-74659600	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:74638200-74659800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:74638200-74660400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:74638200-74660400	Strong transcription	Fetal Thymus	thymus
6	chr5:74638400-74659800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:74638600-74659600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:74638600-74660200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:74638600-74660400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:74638800-74659800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:74639000-74659600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:74639400-74660000	Strong transcription	NHLF	lung
13	chr5:74639400-74660400	Strong transcription	HMEC	breast
14	chr5:74639800-74660000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:74645400-74659800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:74647400-74659800	Strong transcription	GM12878-XiMat	blood
17	chr5:74650000-74659600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:74650000-74660000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:74650200-74659800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:74650400-74660400	Strong transcription	Primary T cells from cord blood	blood
21	chr5:74653000-74659600	Strong transcription	Esophagus	oesophagus
22	chr5:74656000-74659800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:74656000-74659800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:74656400-74665400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:74656400-74669800	Weak transcription	Ovary	ovary
26	chr5:74656400-74670400	Weak transcription	Right Ventricle	heart
27	chr5:74656400-74673600	Weak transcription	Psoas Muscle	Psoas
28	chr5:74656400-74673600	Weak transcription	Small Intestine	intestine
29	chr5:74656400-74673600	Weak transcription	Spleen	Spleen
30	chr5:74656400-74674000	Weak transcription	Brain Germinal Matrix	brain
31	chr5:74656400-74674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:74656400-74674800	Weak transcription	Brain Substantia Nigra	brain
33	chr5:74656400-74676800	Weak transcription	Fetal Brain Male	brain
34	chr5:74656400-74687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:74656600-74660000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:74656600-74668400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:74656600-74670600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:74656600-74675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:74656600-74675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:74656600-74675800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:74656600-74676800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:74656600-74677200	Weak transcription	Aorta	Aorta
44	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
45	chr5:74656800-74660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:74656800-74669600	Weak transcription	Hela-S3	cervix
47	chr5:74656800-74670200	Weak transcription	HepG2	liver
48	chr5:74656800-74670400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr5:74656800-74676200	Weak transcription	Colonic Mucosa	Colon
50	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum

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