Variant report

Variant	rs267736
Chromosome Location	chr1:150945607-150945608
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:150943251-150948012	MCF-7	breast:	n/a	chr1:150946541-150946551 chr1:150947366-150947376 chr1:150944384-150944393 chr1:150946655-150946664
2	NR2F2	chr1:150943257-150945619	MCF-7	breast:	n/a	n/a
3	ZNF263	chr1:150944461-150946776	HEK293-T-REx	kidney:	n/a	chr1:150945506-150945515
4	POLR2A	chr1:150945109-150948108	K562	blood:	n/a	n/a
5	POLR2A	chr1:150945561-150946474	K562	blood:	n/a	n/a
6	MAX	chr1:150945481-150947984	HepG2	liver:	n/a	chr1:150946541-150946551 chr1:150947366-150947376 chr1:150946655-150946664
7	POLR2A	chr1:150943265-150946270	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:150945601-150947608	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:150945575-150946168	HepG2	liver:	n/a	n/a
10	MAX	chr1:150945494-150946907	MCF-7	breast:	n/a	chr1:150946541-150946551 chr1:150946655-150946664
11	MXI1	chr1:150945539-150947660	IMR90	lung:	n/a	n/a
12	POLR2A	chr1:150944933-150945769	PFSK-1	brain:	n/a	n/a
13	NR2F2	chr1:150945537-150946411	K562	blood:	n/a	n/a
14	FOXA1	chr1:150945371-150945746	T-47D	breast:	n/a	n/a
15	CTCF	chr1:150945560-150945710	HCPEpiC	choroid plexus:	n/a	n/a
16	POLR2A	chr1:150945576-150946783	SK-N-MC	brain:	n/a	n/a
17	MXI1	chr1:150942976-150948211	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr1:150945466-150946457	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:150945476-150946914	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150942867..150944822-chr1:150945093..150947347,2	K562	blood:
2	chr1:150897692..150900384-chr1:150944923..150947345,3	K562	blood:
3	chr1:150942078..150949693-chr1:150976791..150984782,24	MCF-7	breast:
4	chr1:150944160..150945692-chr1:151732521..151735210,2	K562	blood:
5	chr1:150532877..150534407-chr1:150944654..150947502,2	MCF-7	breast:
6	chr1:150944222..150949507-chr1:150975860..150982521,8	K562	blood:
7	chr1:150551378..150553300-chr1:150944488..150946159,2	MCF-7	breast:
8	chr1:150945380..150948952-chr1:151032100..151034454,3	K562	blood:
9	chr1:150944409..150948293-chr1:150968315..150970666,3	MCF-7	breast:
10	chr1:150601091..150602624-chr1:150945367..150947119,2	MCF-7	breast:
11	chr1:150667811..150671175-chr1:150944483..150949055,4	MCF-7	breast:
12	chr1:150532195..150535413-chr1:150944658..150948005,3	MCF-7	breast:
13	chr1:150944568..150948169-chr1:151041647..151044581,4	MCF-7	breast:
14	chr1:150943422..150945892-chr1:151029810..151031687,2	MCF-7	breast:
15	chr1:150943930..150948676-chr1:151041268..151044275,5	MCF-7	breast:
16	chr1:150846616..150850276-chr1:150942456..150948926,7	MCF-7	breast:
17	chr1:150800839..150803595-chr1:150945444..150947443,2	K562	blood:
18	chr1:150943913..150947004-chr1:151018258..151022109,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANXA9-1	chr1:150945599-150945645	ENSG00000231073.1

No data

Variant related genes	Relation type
CERS2	TF binding region
ENSG00000143443	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000143437	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000197622	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1112193	0.82[MEX][hapmap]
rs11204727	0.92[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap]
rs11579289	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040707	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12042263	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044969	0.91[ASN][1000 genomes]
rs16832604	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2134688	1.00[CEU][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs2305812	0.93[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs2305815	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs267724	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs267727	0.84[MKK][hapmap]
rs34090972	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738483	1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs3754210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820541	0.91[CEU][hapmap]
rs4379678	0.92[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs533928	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs539118	0.89[ASN][1000 genomes]
rs61817649	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671489	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679701	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs6688248	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72706512	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517566	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs7521445	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7528275	0.82[MEX][hapmap]
rs7535032	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535848	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs771203	0.89[ASN][1000 genomes]
rs771204	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs771205	0.93[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs267736	MRPS21	cis	parietal	SCAN
rs267736	ARNT	cis	parietal	SCAN
rs267736	PIP5K1A	cis	cerebellum	SCAN
rs267736	CA14	cis	cerebellum	SCAN
rs267736	OTUD7B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150942800-150945800	Enhancers	H9 Cell Line	embryonic stem cell
2	chr1:150942800-150945800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:150942800-150945800	Enhancers	Ovary	ovary
4	chr1:150942800-150946000	Flanking Active TSS	Liver	Liver
5	chr1:150942800-150946400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:150943000-150945800	Enhancers	Esophagus	oesophagus
7	chr1:150943000-150946000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:150943000-150946000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:150943200-150945800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:150943200-150945800	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:150943200-150945800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:150943200-150946000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:150943200-150946200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:150943200-150946400	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr1:150943200-150946400	Flanking Active TSS	Osteobl	bone
16	chr1:150943400-150945800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:150943400-150945800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:150943400-150945800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:150943400-150946000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:150943400-150946000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:150943400-150946000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
22	chr1:150943400-150946000	Flanking Active TSS	NHLF	lung
23	chr1:150943400-150946200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:150943400-150946200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:150943400-150946200	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr1:150943400-150946400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:150943400-150946400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr1:150943400-150946400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr1:150943400-150946400	Transcr. at gene 5' and 3'	K562	blood
30	chr1:150943400-150946400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr1:150943400-150946600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:150943600-150945800	Flanking Active TSS	A549	lung
33	chr1:150943600-150946000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr1:150943800-150946000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr1:150944000-150945800	Enhancers	Aorta	Aorta
36	chr1:150944000-150946000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:150944000-150946000	Enhancers	Small Intestine	intestine
38	chr1:150944000-150946400	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr1:150944200-150946000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:150944200-150946000	Flanking Active TSS	Hela-S3	cervix
41	chr1:150944200-150946200	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr1:150944200-150946200	Flanking Active TSS	Fetal Lung	lung
43	chr1:150944200-150946200	Enhancers	Stomach Mucosa	stomach
44	chr1:150944200-150946400	Flanking Active TSS	Colonic Mucosa	Colon
45	chr1:150944200-150946600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr1:150944200-150946600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr1:150944400-150945800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
48	chr1:150944400-150946200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:150944400-150946200	Flanking Active TSS	NH-A	brain
50	chr1:150944400-150946400	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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