Variant report

Variant	rs6672667
Chromosome Location	chr1:150546086-150546087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:122)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr1:150545460-150546134	GM12878	blood:	n/a	chr1:150545489-150545498 chr1:150545486-150545495
2	POLR2A	chr1:150546040-150546267	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:150545420-150546566	GM12891	blood:	n/a	n/a
4	JUND	chr1:150546071-150546242	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:150543194-150546558	HepG2	liver:	n/a	n/a
6	MTA3	chr1:150544950-150546278	GM12878	blood:	n/a	n/a
7	CREB1	chr1:150545416-150546280	K562	blood:	n/a	n/a
8	ATF2	chr1:150545129-150546556	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
10	CCNT2	chr1:150545457-150546315	K562	blood:	n/a	n/a
11	POLR2A	chr1:150544288-150546564	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
13	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
14	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
15	CHD2	chr1:150544925-150546197	K562	blood:	n/a	n/a
16	POLR2A	chr1:150541963-150546408	HUVEC	blood vessel:	n/a	n/a
17	TEAD4	chr1:150544936-150546577	K562	blood:	n/a	n/a
18	NFATC1	chr1:150545293-150546213	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:150543224-150546653	K562	blood:	n/a	n/a
20	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
21	SIN3AK20	chr1:150543601-150546543	K562	blood:	n/a	n/a
22	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
23	POU2F2	chr1:150545494-150546201	GM12891	blood:	n/a	chr1:150545873-150545885 chr1:150545875-150545886 chr1:150545873-150545886 chr1:150545874-150545884 chr1:150545872-150545887 chr1:150545875-150545885 chr1:150545876-150545884 chr1:150545871-150545889 chr1:150545874-150545884
24	POU2F2	chr1:150545398-150546416	GM12891	blood:	n/a	chr1:150545873-150545885 chr1:150545875-150545886 chr1:150545873-150545886 chr1:150545874-150545884 chr1:150545872-150545887 chr1:150545875-150545885 chr1:150545876-150545884 chr1:150545871-150545889 chr1:150545874-150545884
25	POLR2A	chr1:150540216-150546538	U87	brain:	n/a	n/a
26	POLR2A	chr1:150544471-150546444	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:150545405-150546201	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
29	EGR1	chr1:150545493-150546190	K562	blood:	n/a	n/a
30	YY1	chr1:150546040-150546246	K562	blood:	n/a	n/a
31	POLR2A	chr1:150544818-150546306	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr1:150543314-150546680	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:150545436-150546521	HL-60	blood:	n/a	n/a
35	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a
38	POLR2A	chr1:150538945-150546560	HUVEC	blood vessel:	n/a	n/a
39	TAF1	chr1:150545557-150546254	K562	blood:	n/a	n/a
40	POLR2A	chr1:150544980-150546467	K562	blood:	n/a	n/a
41	POLR2A	chr1:150545134-150546224	GM15510	blood:	n/a	n/a
42	POLR2A	chr1:150542302-150546578	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr1:150538877-150553278	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:150538822-150553196	H1-hESC	embryonic stem cell:	n/a	n/a
45	TAF7	chr1:150545105-150546508	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:150546041-150546260	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr1:150542706-150546537	K562	blood:	n/a	n/a
48	POLR2A	chr1:150543438-150546395	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:150544939-150546549	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:150542040-150546487	GM12891	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150258806..150260952-chr1:150544503..150546807,2	K562	blood:
2	chr1:150545934..150547649-chr1:150567302..150569853,2	K562	blood:
3	chr1:150455770..150459652-chr1:150544183..150547234,4	K562	blood:
4	chr1:150543953..150547860-chr1:150600449..150605575,7	K562	blood:
5	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
6	chr1:150543938..150548482-chr1:150576509..150579510,5	K562	blood:
7	chr1:150545565..150549511-chr1:150783335..150787451,6	K562	blood:
8	chr1:150545938..150547543-chr1:150804208..150806124,2	K562	blood:
9	chr1:150544693..150547632-chr1:150583989..150587707,3	MCF-7	breast:
10	chr1:150544010..150546916-chr1:150590925..150592477,2	MCF-7	breast:
11	chr1:150543916..150546115-chr1:150744599..150746718,2	K562	blood:
12	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
13	chr1:150545107..150547028-chr1:150615492..150618208,2	K562	blood:
14	chr1:150545938..150548404-chr1:150780767..150782416,2	K562	blood:
15	chr1:150545388..150547945-chr1:150570621..150572716,2	K562	blood:
16	chr1:150455770..150457599-chr1:150544025..150546783,3	K562	blood:
17	chr1:150545613..150547144-chr1:150678229..150680325,2	K562	blood:
18	chr1:150435919..150438376-chr1:150544338..150547064,3	K562	blood:
19	chr1:150545560..150548928-chr1:150668482..150671179,4	K562	blood:
20	chr1:150545274..150547768-chr1:150592688..150595152,4	MCF-7	breast:

No data

Variant related genes	Relation type
RN7SL600P	TF binding region
ENSG00000143387	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000143452	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1053701	0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11204665	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204674	1.00[AMR][1000 genomes]
rs11204689	0.93[AMR][1000 genomes]
rs11585460	0.85[ASN][1000 genomes]
rs12031458	0.93[AMR][1000 genomes]
rs12032445	0.93[AMR][1000 genomes]
rs12034302	0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12036914	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038403	0.93[AMR][1000 genomes]
rs12042580	0.87[ASN][1000 genomes]
rs12045807	0.82[ASN][1000 genomes]
rs28744536	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754207	0.93[AMR][1000 genomes]
rs55890313	0.93[AMR][1000 genomes]
rs60060012	0.88[ASN][1000 genomes]
rs61820166	0.88[ASN][1000 genomes]
rs61820168	0.87[ASN][1000 genomes]
rs61820170	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6587515	0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7517	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs7543465	0.98[EUR][1000 genomes];0.95[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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6672667	ARNT	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150541400-150547200	Genic enhancers	Fetal Intestine Small	intestine
3	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:150541800-150546800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:150542000-150547200	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:150542200-150547200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:150542200-150547200	Strong transcription	Brain Germinal Matrix	brain
8	chr1:150542200-150548000	Genic enhancers	Placenta	Placenta
9	chr1:150542400-150546800	Genic enhancers	Fetal Muscle Leg	muscle
10	chr1:150542400-150547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:150542600-150547200	Genic enhancers	Lung	lung
12	chr1:150542600-150548200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:150542800-150547800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:150542800-150551600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
15	chr1:150543000-150549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:150543200-150547000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:150543400-150547000	Genic enhancers	Osteobl	bone
18	chr1:150543600-150547200	Genic enhancers	Dnd41	blood
19	chr1:150543600-150547800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:150543600-150548200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
23	chr1:150543600-150552000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:150543800-150547000	Strong transcription	Fetal Lung	lung
25	chr1:150544000-150547000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:150544000-150547200	Strong transcription	Fetal Stomach	stomach
27	chr1:150544000-150547400	Weak transcription	Fetal Brain Male	brain
28	chr1:150544200-150551600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
29	chr1:150544400-150546400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:150544400-150547200	Genic enhancers	Fetal Intestine Large	intestine
31	chr1:150544600-150551600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
32	chr1:150544800-150546800	Genic enhancers	HUVEC	blood vessel
33	chr1:150544800-150547000	Genic enhancers	Left Ventricle	heart
34	chr1:150544800-150548400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:150545000-150546200	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
36	chr1:150545000-150546200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
37	chr1:150545000-150546600	Genic enhancers	Colonic Mucosa	Colon
38	chr1:150545000-150546800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:150545000-150546800	Genic enhancers	HMEC	breast
40	chr1:150545000-150547200	Genic enhancers	A549	lung
41	chr1:150545000-150548600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:150545000-150550000	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
43	chr1:150545000-150551400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
44	chr1:150545200-150546200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:150545200-150546200	Genic enhancers	Colon Smooth Muscle	Colon
46	chr1:150545200-150546400	Transcr. at gene 5' and 3'	NH-A	brain
47	chr1:150545200-150546600	Strong transcription	Fetal Kidney	kidney
48	chr1:150545200-150547000	Genic enhancers	Hela-S3	cervix
49	chr1:150545200-150547200	Genic enhancers	Brain Anterior Caudate	brain
50	chr1:150545200-150547200	Genic enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links