Variant report

Variant	rs11264736
Chromosome Location	chr1:153939130-153939131
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	POLR2A	chr1:153938950-153940700	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:153939130-153939261	HUVEC	blood vessel:	n/a	n/a
3	RFX5	chr1:153939044-153940690	Hela-S3	cervix:	n/a	n/a
4	MAX	chr1:153939071-153940597	Hela-S3	cervix:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
5	SPI1	chr1:153939122-153939252	GM12878	blood:	n/a	n/a
6	JUN	chr1:153938999-153941490	K562	blood:	n/a	chr1:153940887-153940896 chr1:153940888-153940897
7	SIN3AK20	chr1:153939018-153941202	MCF-7	breast:	n/a	n/a
8	KAP1	chr1:153939098-153940614	U2OS	brain:	n/a	n/a
9	NFIC	chr1:153939063-153940549	GM12878	blood:	n/a	n/a
10	MYC	chr1:153939115-153941357	K562	blood:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
11	POLR2A	chr1:153939091-153940597	K562	blood:	n/a	n/a
12	MAFK	chr1:153939097-153940704	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:153938347-153939375	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:153939130-153940820	PBDE	blood:	n/a	n/a
15	POLR2A	chr1:153938327-153941368	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr1:153939077-153939350	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr1:153938969-153941793	SK-N-SH	brain:	n/a	chr1:153939837-153939846
18	CHD1	chr1:153939089-153940177	GM12878	blood:	n/a	n/a
19	SPI1	chr1:153939080-153939349	HL-60	blood:	n/a	n/a
20	POLR2A	chr1:153939124-153939136	Hela-S3	cervix:	n/a	n/a
21	TRIM28	chr1:153939106-153940414	K562	blood:	n/a	n/a
22	RCOR1	chr1:153938977-153940566	Hela-S3	cervix:	n/a	n/a
23	STAT3	chr1:153939099-153940559	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:153939088-153940613	K562	blood:	n/a	n/a
25	POLR2A	chr1:153938953-153940624	PANC-1	pancreas:	n/a	n/a
26	SPI1	chr1:153939043-153939364	GM12878	blood:	n/a	n/a
27	MTA3	chr1:153938335-153940835	GM12878	blood:	n/a	n/a
28	HCFC1	chr1:153938960-153941500	Hela-S3	cervix:	n/a	n/a
29	SPI1	chr1:153939030-153939277	K562	blood:	n/a	n/a
30	MXI1	chr1:153939080-153940576	GM12878	blood:	n/a	chr1:153939837-153939846
31	POLR2A	chr1:153938967-153939258	Hela-S3	cervix:	n/a	n/a
32	MXI1	chr1:153938962-153939301	Hela-S3	cervix:	n/a	n/a
33	MYC	chr1:153939098-153940742	A549	lung:	n/a	chr1:153939838-153939847 chr1:153939837-153939848 chr1:153939838-153939847 chr1:153939833-153939852 chr1:153939836-153939849
34	POLR2A	chr1:153939111-153940961	HCT-116	colon:	n/a	n/a
35	POLR2A	chr1:153939050-153940975	Hela-S3	cervix:	n/a	n/a
36	MAX	chr1:153938577-153939198	K562	blood:	n/a	n/a
37	TEAD4	chr1:153938970-153940640	K562	blood:	n/a	n/a
38	SIN3AK20	chr1:153939063-153940795	MCF-7	breast:	n/a	n/a
39	POLR2A	chr1:153938315-153941481	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr1:153938369-153941146	GM12891	blood:	n/a	n/a
41	SPI1	chr1:153939054-153939417	HL-60	blood:	n/a	n/a
42	POLR2A	chr1:153938479-153940748	K562	blood:	n/a	n/a
43	IRF1	chr1:153939085-153940544	K562	blood:	n/a	n/a
44	CTCF	chr1:153939040-153940751	A549	lung:	n/a	chr1:153939750-153939763
45	POLR2A	chr1:153938963-153939275	Hela-S3	cervix:	n/a	n/a
46	FOS	chr1:153939112-153939188	MCF10A-Er-Src	breast:	n/a	n/a
47	MAFK	chr1:153939094-153939133	HepG2	liver:	n/a	n/a
48	POLR2A	chr1:153939108-153941161	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:153938949-153940897	GM18505	blood:	n/a	n/a
50	POLR2A	chr1:153938589-153941307	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153936330..153941464-chr1:154191669..154195552,8	MCF-7	breast:
2	chr1:153605540..153608540-chr1:153937612..153940414,3	MCF-7	breast:
3	chr1:153938901..153941053-chr16:89004507..89006484,2	MCF-7	breast:
4	chr1:153641625..153644878-chr1:153937648..153941391,3	K562	blood:
5	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
6	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
7	chr1:153640832..153646304-chr1:153937039..153940655,5	MCF-7	breast:
8	chr1:153938202..153942686-chr1:154154566..154158952,5	MCF-7	breast:
9	chr1:153599605..153601359-chr1:153938449..153940087,2	MCF-7	breast:
10	chr1:153747310..153750060-chr1:153937716..153939765,3	MCF-7	breast:
11	chr1:153939104..153942755-chr1:154191760..154194945,4	MCF-7	breast:
12	chr1:153938923..153939839-chr3:38206200..38207525,3	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CREB3L4-3	chr1:153938992-153939406	ENSG00000273026.1

Variant related genes	Relation type
CREB3L4	TF binding region
SLC39A1	TF binding region
ENSG00000272030	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000261226	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000205018	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000172939	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000189171	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10127484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908525	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908526	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908578	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs11264573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264621	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11800001	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12124424	0.81[AFR][1000 genomes]
rs12130611	0.80[AFR][1000 genomes]
rs12142639	0.86[ASN][1000 genomes]
rs12142733	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs17364880	1.00[JPT][hapmap]
rs2252508	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2790686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.83[YRI][hapmap]
rs2790690	0.83[YRI][hapmap]
rs2841108	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.81[YRI][hapmap]
rs3001365	1.00[CHB][hapmap]
rs35711150	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791186	0.84[EUR][1000 genomes]
rs4276953	0.80[EUR][1000 genomes]
rs4370789	0.81[AFR][1000 genomes]
rs4845360	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4845586	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6427300	0.81[AFR][1000 genomes]
rs6661009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671362	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7414227	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521047	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs7522030	0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7537213	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs7549032	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7554469	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' 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 miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lentiform nucleus volume	22903471	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11264736	S100A8	cis	parietal	SCAN
rs11264736	HAX1	cis	cerebellum	SCAN
rs11264736	GATAD2B	cis	cerebellum	SCAN
rs11264736	PSMD4	cis	parietal	SCAN
rs11264736	FLG	cis	parietal	SCAN
rs11264736	GBA	cis	parietal	SCAN
rs11264736	SLC27A3	cis	cerebellum	SCAN
rs11264736	CTAG2	trans	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153936800-153939200	Weak transcription	Aorta	Aorta
2	chr1:153936800-153939200	Weak transcription	Ovary	ovary
3	chr1:153936800-153939600	Weak transcription	Gastric	stomach
4	chr1:153936800-153939600	Weak transcription	Small Intestine	intestine
5	chr1:153937000-153939200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:153937000-153939200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:153937000-153939200	Enhancers	Fetal Brain Male	brain
8	chr1:153937000-153939400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:153937000-153939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:153937000-153939600	Weak transcription	Esophagus	oesophagus
11	chr1:153937200-153939200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:153937200-153939200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:153937400-153939400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:153937400-153939400	Weak transcription	Left Ventricle	heart
15	chr1:153937400-153939600	Weak transcription	Lung	lung
16	chr1:153937600-153939200	Enhancers	Placenta	Placenta
17	chr1:153937800-153939400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:153938000-153939200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:153938000-153939200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:153938200-153939200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:153938200-153939400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr1:153938400-153939200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:153938400-153939200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr1:153938400-153939200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:153938400-153939200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:153938400-153939200	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:153938400-153939200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr1:153938400-153939200	Flanking Active TSS	Fetal Thymus	thymus
29	chr1:153938400-153939200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr1:153938400-153939200	Enhancers	Stomach Mucosa	stomach
31	chr1:153938400-153939400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr1:153938400-153939400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:153938400-153939400	Flanking Active TSS	Colonic Mucosa	Colon
34	chr1:153938400-153939400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr1:153938400-153939400	Flanking Active TSS	Thymus	Thymus
36	chr1:153938400-153939400	Flanking Active TSS	Dnd41	blood
37	chr1:153938400-153939400	Flanking Active TSS	Hela-S3	cervix
38	chr1:153938400-153939600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr1:153938400-153939600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr1:153938400-153939600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr1:153938400-153939600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:153938400-153939800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:153938400-153940000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:153938400-153941000	Active TSS	A549	lung
45	chr1:153938400-153941400	Active TSS	H9 Cell Line	embryonic stem cell
46	chr1:153938600-153939200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:153938600-153939200	Enhancers	Brain Anterior Caudate	brain
48	chr1:153938600-153939200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:153938600-153939200	Enhancers	Fetal Lung	lung
50	chr1:153938600-153939200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links