Variant report

Variant	rs461404
Chromosome Location	chr5:40799540-40799541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr5:40799468-40800598	K562	blood:	n/a	n/a
2	CTCF	chr5:40798095-40799543	K562	blood:	n/a	chr5:40798438-40798451 chr5:40798442-40798451 chr5:40798589-40798598
3	TBL1XR1	chr5:40797271-40799794	K562	blood:	n/a	n/a
4	RCOR1	chr5:40797576-40800142	K562	blood:	n/a	n/a
5	TBP	chr5:40799485-40799842	K562	blood:	n/a	n/a
6	ARID3A	chr5:40798896-40799811	K562	blood:	n/a	n/a
7	RFX5	chr5:40797380-40799619	Hela-S3	cervix:	n/a	chr5:40797938-40797953 chr5:40797937-40797954 chr5:40798991-40798999 chr5:40797938-40797953 chr5:40797938-40797953
8	BRCA1	chr5:40797611-40799729	Hela-S3	cervix:	n/a	n/a
9	EP300	chr5:40797373-40799970	K562	blood:	n/a	chr5:40798444-40798460 chr5:40797855-40797864 chr5:40797823-40797832 chr5:40799242-40799252 chr5:40798012-40798028 chr5:40797852-40797868
10	IRF1	chr5:40798005-40800385	K562	blood:	n/a	chr5:40799755-40799767 chr5:40798104-40798121 chr5:40799756-40799766 chr5:40799752-40799766 chr5:40798849-40798863 chr5:40799756-40799770 chr5:40799977-40799991
11	EP300	chr5:40798875-40799694	Hela-S3	cervix:	n/a	chr5:40799242-40799252
12	CEBPB	chr5:40798939-40799823	K562	blood:	n/a	chr5:40799675-40799688
13	MXI1	chr5:40797436-40799625	K562	blood:	n/a	chr5:40797937-40797952 chr5:40797939-40797954
14	RFX5	chr5:40798997-40799781	K562	blood:	n/a	n/a
15	RCOR1	chr5:40799338-40799661	K562	blood:	n/a	n/a
16	MYC	chr5:40799391-40800085	K562	blood:	n/a	n/a
17	ZMIZ1	chr5:40798015-40799809	K562	blood:	n/a	n/a
18	CHD2	chr5:40799526-40799639	K562	blood:	n/a	n/a
19	TEAD4	chr5:40799306-40800195	K562	blood:	n/a	n/a
20	TBP	chr5:40798655-40799703	Hela-S3	cervix:	n/a	n/a
21	BHLHE40	chr5:40797393-40799711	K562	blood:	n/a	chr5:40798450-40798466 chr5:40798005-40798021
22	EP300	chr5:40798931-40799664	K562	blood:	n/a	chr5:40799242-40799252
23	TAL1	chr5:40799436-40799776	K562	blood:	n/a	n/a
24	UBTF	chr5:40797166-40799688	K562	blood:	n/a	n/a
25	CUX1	chr5:40798102-40800290	K562	blood:	n/a	chr5:40799160-40799174
26	IRF1	chr5:40799386-40800424	K562	blood:	n/a	chr5:40799755-40799767 chr5:40799756-40799766 chr5:40800401-40800413 chr5:40799752-40799766 chr5:40799756-40799770 chr5:40799977-40799991
27	CEBPB	chr5:40797517-40799752	Hela-S3	cervix:	n/a	chr5:40799675-40799688

No.	Distal block	Cell Line	Cell type
1	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
2	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
3	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
4	chr5:40771302..40774054-chr5:40798979..40801036,2	K562	blood:
5	chr5:40778589..40781833-chr5:40798494..40800242,3	K562	blood:
6	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
7	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
8	chr5:40778589..40781225-chr5:40798736..40800242,2	K562	blood:

Variant related genes	Relation type
PRKAA1	TF binding region
ENSG00000113638	Chromatin interaction
ENSG00000212296	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000132356	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10056345	0.85[ASN][1000 genomes]
rs10060234	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs10064175	0.81[ASN][1000 genomes]
rs1070446	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs1097546	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155724	0.81[CEU][hapmap]
rs13167906	0.82[CEU][hapmap]
rs13355305	0.85[ASN][1000 genomes]
rs154268	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154275	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154280	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154281	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154284	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171605	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171606	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs192219	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs193864	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193866	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2008763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161521	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249413	0.85[ASN][1000 genomes]
rs249414	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs249416	0.87[ASN][1000 genomes]
rs249420	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249422	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249423	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249425	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249429	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249437	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249438	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs249441	0.80[ASN][1000 genomes]
rs257009	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569300	0.85[ASN][1000 genomes]
rs29740	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29742	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29743	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29744	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29761	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
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	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434778	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs4383756	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs447810	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs453037	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457776	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs466108	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466962	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.85[ASN][1000 genomes]
rs4957351	0.81[EUR][1000 genomes]
rs59069340	0.85[ASN][1000 genomes]
rs59920139	0.85[ASN][1000 genomes]
rs6451535	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs6451537	0.85[ASN][1000 genomes]
rs6871999	0.85[ASN][1000 genomes]
rs6896993	0.85[ASN][1000 genomes]
rs6897470	0.83[EUR][1000 genomes]
rs7708680	0.85[ASN][1000 genomes]
rs7711806	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726237	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs7737044	0.85[ASN][1000 genomes]
rs837101	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs461404	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs461404	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL
rs461404	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs461404	FBXO4	cis	parietal	SCAN
rs461404		cis	Lymphoblastoid	GTEx
rs461404	RPL37	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40795800-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:40796200-40799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:40796200-40799600	Active TSS	Fetal Intestine Large	intestine
4	chr5:40796400-40800000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:40796400-40800000	Active TSS	NHLF	lung
6	chr5:40796600-40799600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:40796600-40799600	Active TSS	Ovary	ovary
8	chr5:40796600-40799800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:40796600-40799800	Active TSS	Fetal Kidney	kidney
10	chr5:40796600-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:40796600-40800400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr5:40796800-40799600	Active TSS	NHDF-Ad	bronchial
13	chr5:40797000-40799800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:40797000-40800000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:40797200-40799600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr5:40797200-40799800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr5:40797200-40800000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:40797400-40799800	Active TSS	Brain Anterior Caudate	brain
19	chr5:40797600-40799600	Active TSS	Brain Hippocampus Middle	brain
20	chr5:40798600-40799800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:40798600-40799800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:40798800-40799800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr5:40798800-40800200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:40799000-40799600	Flanking Active TSS	Fetal Brain Female	brain
25	chr5:40799000-40799800	Enhancers	Stomach Mucosa	stomach
26	chr5:40799000-40800000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr5:40799000-40800000	Flanking Active TSS	Hela-S3	cervix
28	chr5:40799000-40800000	Flanking Active TSS	HUVEC	blood vessel
29	chr5:40799200-40799600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr5:40799200-40799600	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:40799200-40799600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:40799200-40799600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:40799200-40799600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:40799200-40799600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:40799200-40799600	Enhancers	Duodenum Mucosa	Duodenum
36	chr5:40799200-40799600	Enhancers	Rectal Smooth Muscle	rectum
37	chr5:40799200-40799800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:40799200-40799800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:40799200-40799800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr5:40799200-40799800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:40799200-40799800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr5:40799200-40799800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr5:40799200-40799800	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:40799200-40799800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:40799200-40799800	Enhancers	Brain Substantia Nigra	brain
46	chr5:40799200-40799800	Enhancers	Fetal Heart	heart
47	chr5:40799200-40799800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr5:40799200-40799800	Flanking Active TSS	HepG2	liver
49	chr5:40799200-40799800	Enhancers	NHEK	skin
50	chr5:40799200-40799800	Enhancers	Osteobl	bone

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