Variant report

Variant	rs7533689
Chromosome Location	chr1:212588695-212588696
allele	A/G
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	MYC	chr1:212587629-212589222	NB4	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
2	BCLAF1	chr1:212587946-212588696	GM12878	blood:	n/a	chr1:212588411-212588420 chr1:212587983-212587992 chr1:212588261-212588274
3	TEAD4	chr1:212588004-212589288	K562	blood:	n/a	n/a
4	EP300	chr1:212588106-212588711	GM12878	blood:	n/a	chr1:212588411-212588425
5	CHD2	chr1:212588043-212589141	GM12878	blood:	n/a	n/a
6	MAX	chr1:212587315-212589069	GM12878	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
7	NFIC	chr1:212588085-212589257	GM12878	blood:	n/a	n/a
8	BCLAF1	chr1:212587937-212588751	GM12878	blood:	n/a	chr1:212588411-212588420 chr1:212587983-212587992 chr1:212588261-212588274
9	POLR2A	chr1:212587788-212588758	K562	blood:	n/a	n/a
10	HCFC1	chr1:212587426-212589189	K562	blood:	n/a	n/a
11	POLR2A	chr1:212587484-212589250	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:212587954-212589321	HL-60	blood:	n/a	n/a
13	SREBP1	chr1:212587176-212589923	GM12878	blood:	n/a	n/a
14	WRNIP1	chr1:212588225-212589185	GM12878	blood:	n/a	n/a
15	CEBPB	chr1:212588000-212589247	GM12878	blood:	n/a	n/a
16	CBX3	chr1:212587912-212589221	K562	blood:	n/a	n/a
17	NFIC	chr1:212588107-212588720	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:212587655-212589175	GM19193	blood:	n/a	n/a
19	POLR2A	chr1:212587714-212588704	GM12892	blood:	n/a	n/a
20	TBL1XR1	chr1:212588098-212588862	GM12878	blood:	n/a	n/a
21	NFATC1	chr1:212587990-212589147	GM12878	blood:	n/a	n/a
22	BHLHE40	chr1:212588036-212589170	K562	blood:	n/a	chr1:212588255-212588271
23	MAX	chr1:212587427-212589193	NB4	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
24	IRF4	chr1:212588120-212588708	GM12878	blood:	n/a	n/a
25	JUN	chr1:212586575-212589515	K562	blood:	n/a	chr1:212587985-212587994 chr1:212589466-212589475
26	MAX	chr1:212587497-212588710	H1-hESC	embryonic stem cell:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
27	POLR2A	chr1:212587590-212588744	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:212587788-212589160	GM12891	blood:	n/a	n/a
29	MXI1	chr1:212586634-212588790	SK-N-SH	brain:	n/a	n/a
30	FOXM1	chr1:212587882-212589328	GM12878	blood:	n/a	n/a
31	HCFC1	chr1:212586968-212588965	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:212587494-212589159	GM12892	blood:	n/a	n/a
33	REST	chr1:212587703-212588759	H1-neurons	neurons:	n/a	chr1:212587970-212587983
34	POLR2A	chr1:212587768-212589166	NB4	blood:	n/a	n/a
35	POLR2A	chr1:212587821-212589244	GM12878	blood:	n/a	n/a
36	ZNF143	chr1:212587486-212588798	H1-hESC	embryonic stem cell:	n/a	chr1:212588298-212588307 chr1:212588296-212588305 chr1:212587976-212587994
37	STAT5A	chr1:212587685-212589154	GM12878	blood:	n/a	n/a
38	RUNX3	chr1:212587429-212589362	GM12878	blood:	n/a	n/a
39	NR2F2	chr1:212587571-212589354	K562	blood:	n/a	n/a
40	ZNF143	chr1:212588058-212589043	K562	blood:	n/a	chr1:212588298-212588307 chr1:212588296-212588305
41	POLR2A	chr1:212588077-212589029	PBDE	blood:	n/a	n/a
42	POLR2A	chr1:212587933-212588707	Raji	blood:	n/a	n/a
43	STAT1	chr1:212588160-212588748	GM12878	blood:	n/a	n/a
44	RELA	chr1:212588214-212589036	GM19099	blood:	n/a	n/a
45	NRF1	chr1:212587879-212588859	SK-N-SH	brain:	n/a	chr1:212588245-212588259 chr1:212588250-212588259 chr1:212588247-212588258 chr1:212588248-212588257 chr1:212588248-212588259
46	STAT5A	chr1:212588053-212588742	GM12878	blood:	n/a	n/a
47	REST	chr1:212588148-212589271	HL-60	blood:	n/a	n/a
48	EP300	chr1:212588076-212588816	GM12878	blood:	n/a	chr1:212588411-212588425
49	ATF2	chr1:212588062-212588986	GM12878	blood:	n/a	n/a
50	SPI1	chr1:212587991-212589166	HL-60	blood:	n/a	chr1:212588413-212588426 chr1:212588507-212588516 chr1:212588508-212588515 chr1:212588414-212588427 chr1:212588416-212588423 chr1:212588411-212588420 chr1:212589026-212589033

No.	Distal block	Cell Line	Cell type
1	chr1:212588338..212589858-chr1:212645243..212647080,2	K562	blood:
2	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
3	chr1:212586222..212588940-chr1:212781343..212783037,2	K562	blood:
4	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
5	chr1:212588056..212590074-chr1:212779163..212783567,3	K562	blood:
6	chr1:212549233..212551182-chr1:212586836..212589324,2	K562	blood:
7	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
8	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
9	chr1:212581574..212584496-chr1:212586803..212589409,2	MCF-7	breast:

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000203705	Chromatin interaction
ENSG00000117691	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10494951	0.81[TSI][hapmap]
rs11590242	0.81[TSI][hapmap]
rs11803766	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739715	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12755383	1.00[EUR][1000 genomes]
rs17018997	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2120770	0.84[TSI][hapmap]
rs35702733	0.99[EUR][1000 genomes]
rs35822123	0.83[EUR][1000 genomes]
rs3767867	0.80[GIH][hapmap]
rs4336916	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4540733	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6666415	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669027	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6676208	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs6693849	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6697910	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704234	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71646158	0.83[EUR][1000 genomes]
rs71646159	0.94[EUR][1000 genomes]
rs71646161	1.00[EUR][1000 genomes]
rs7518399	0.83[TSI][hapmap]
rs7551910	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7533689	RP11-15I11.3	cis	lung	GTEx
rs7533689	BATF3	cis	cerebellum	SCAN
rs7533689	ATF3	cis	parietal	SCAN
rs7533689	C1orf74	cis	parietal	SCAN
rs7533689	RP11-15I11.3	cis	Thyroid	GTEx
rs7533689	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212587000-212588800	Enhancers	Fetal Heart	heart
2	chr1:212587000-212589000	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:212587400-212589000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:212587600-212588800	Active TSS	Spleen	Spleen
5	chr1:212587800-212588800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:212587800-212588800	Active TSS	Colonic Mucosa	Colon
7	chr1:212587800-212589000	Active TSS	Stomach Smooth Muscle	stomach
8	chr1:212588200-212588800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:212588200-212589000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:212588200-212589000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:212588200-212589000	Flanking Active TSS	Brain Substantia Nigra	brain
12	chr1:212588200-212589000	Flanking Active TSS	Dnd41	blood
13	chr1:212588200-212589200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr1:212588400-212588800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:212588400-212588800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212588400-212588800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:212588400-212588800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:212588400-212588800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:212588400-212588800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:212588400-212588800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr1:212588400-212588800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr1:212588400-212588800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:212588400-212588800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr1:212588400-212588800	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr1:212588400-212588800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:212588400-212588800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:212588400-212589000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:212588400-212589000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:212588400-212589000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:212588400-212589000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:212588400-212589000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr1:212588400-212589000	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr1:212588400-212589000	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr1:212588400-212589000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:212588400-212589000	Flanking Active TSS	K562	blood
36	chr1:212588400-212589200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr1:212588400-212589200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:212588400-212589200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:212588400-212589200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:212588400-212589200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:212588400-212589200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:212588400-212589200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:212588400-212589200	Flanking Active TSS	HepG2	liver
44	chr1:212588400-212589200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr1:212588400-212589400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:212588400-212590200	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:212588400-212590600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:212588600-212588800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr1:212588600-212588800	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:212588600-212588800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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