Variant report

Variant	rs154284
Chromosome Location	chr5:40788574-40788575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40772744..40775681-chr5:40786682..40789617,2	K562	blood:
2	chr5:40785220..40789232-chr5:40791780..40795190,3	K562	blood:
3	chr5:40773990..40775613-chr5:40787064..40789947,2	MCF-7	breast:
4	chr5:40786316..40788654-chr5:40789788..40791348,2	K562	blood:

Variant related genes	Relation type
ENSG00000212567	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10056345	0.85[ASN][1000 genomes]
rs10060234	0.85[ASN][1000 genomes]
rs10064175	0.81[ASN][1000 genomes]
rs1097546	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355305	0.85[ASN][1000 genomes]
rs154268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154275	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154280	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154281	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171605	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171606	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193864	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008763	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161521	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249413	0.85[ASN][1000 genomes]
rs249414	0.87[ASN][1000 genomes]
rs249416	0.87[ASN][1000 genomes]
rs249420	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249422	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249423	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249425	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249428	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249429	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249437	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249438	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs249441	0.80[ASN][1000 genomes]
rs257009	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569300	0.85[ASN][1000 genomes]
rs29740	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29742	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29743	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29744	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277957	0.85[ASN][1000 genomes]
rs4285273	0.85[ASN][1000 genomes]
rs4315964	0.85[ASN][1000 genomes]
rs4315965	0.85[ASN][1000 genomes]
rs432071	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434778	0.89[ASN][1000 genomes]
rs4383756	0.85[ASN][1000 genomes]
rs447810	0.89[ASN][1000 genomes]
rs453037	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461404	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466108	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466962	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.85[ASN][1000 genomes]
rs4957351	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59069340	0.85[ASN][1000 genomes]
rs59920139	0.85[ASN][1000 genomes]
rs6451535	0.83[ASN][1000 genomes]
rs6451537	0.85[ASN][1000 genomes]
rs6871999	0.85[ASN][1000 genomes]
rs6896993	0.85[ASN][1000 genomes]
rs6897470	0.82[EUR][1000 genomes]
rs7708680	0.85[ASN][1000 genomes]
rs7711806	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726237	0.83[ASN][1000 genomes]
rs7737044	0.85[ASN][1000 genomes]
rs837101	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs154284	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs154284	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL
rs154284	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
4	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:40771600-40788600	Weak transcription	Fetal Stomach	stomach
6	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
7	chr5:40777000-40789400	Weak transcription	Fetal Heart	heart
8	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
10	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:40777200-40791400	Weak transcription	Brain Angular Gyrus	brain
13	chr5:40777200-40796000	Weak transcription	Lung	lung
14	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
15	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:40777600-40789400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:40777600-40792000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:40777600-40792800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:40777600-40795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:40777600-40795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:40777800-40789600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr5:40777800-40795600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr5:40777800-40796600	Weak transcription	NH-A	brain
24	chr5:40778000-40795400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:40781000-40791200	Weak transcription	NHEK	skin
26	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
27	chr5:40782400-40790000	Weak transcription	Left Ventricle	heart
28	chr5:40782400-40791400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:40782400-40795600	Weak transcription	NHLF	lung
30	chr5:40782600-40788600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:40782600-40790200	Weak transcription	Adipose Nuclei	Adipose
32	chr5:40782600-40791200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:40782600-40791200	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:40783000-40795600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:40783800-40795600	Weak transcription	Ovary	ovary
36	chr5:40785000-40792800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:40785000-40795400	Weak transcription	Pancreas	Pancrea
38	chr5:40785200-40795200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr5:40786000-40791000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:40786000-40791000	Weak transcription	Fetal Intestine Large	intestine
41	chr5:40786000-40791000	Weak transcription	Small Intestine	intestine
42	chr5:40786000-40791400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:40786200-40789400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:40786200-40795600	Weak transcription	Psoas Muscle	Psoas
45	chr5:40786400-40790200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:40786800-40790400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:40787000-40788600	Weak transcription	Fetal Intestine Small	intestine
48	chr5:40787000-40788800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:40787200-40790600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:40787600-40788600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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