Variant report

Variant	rs74051540
Chromosome Location	chr1:9599179-9599180
allele	A/C
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	SETDB1	chr1:9599060-9599468	U2OS	brain:	n/a	n/a
2	ZBTB33	chr1:9599040-9599537	GM12878	blood:	n/a	chr1:9599251-9599261
3	EP300	chr1:9599145-9599677	H1-hESC	embryonic stem cell:	n/a	chr1:9599488-9599497
4	PML	chr1:9598935-9599834	GM12878	blood:	n/a	chr1:9599261-9599269
5	ATF2	chr1:9599023-9599571	H1-hESC	embryonic stem cell:	n/a	chr1:9599473-9599484
6	POLR2A	chr1:9599088-9600511	GM12892	blood:	n/a	n/a
7	MAZ	chr1:9599097-9600267	GM12878	blood:	n/a	chr1:9599495-9599506 chr1:9599496-9599505 chr1:9599972-9599982 chr1:9599496-9599505 chr1:9599498-9599514 chr1:9599490-9599500 chr1:9599700-9599709
8	HA-E2F1	chr1:9599091-9600465	MCF-7	breast:	n/a	chr1:9600151-9600160 chr1:9599918-9599927 chr1:9600034-9600043 chr1:9599739-9599748 chr1:9599473-9599482 chr1:9600148-9600160 chr1:9599475-9599484
9	TBP	chr1:9599074-9599668	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:9599038-9599755	H1-neurons	neurons:	n/a	n/a
11	RFX5	chr1:9599135-9599690	Hela-S3	cervix:	n/a	chr1:9599409-9599418
12	E2F6	chr1:9598943-9599723	H1-hESC	embryonic stem cell:	n/a	chr1:9599473-9599482 chr1:9599475-9599484
13	POLR2A	chr1:9599142-9599387	GM12891	blood:	n/a	n/a
14	MYBL2	chr1:9598964-9599586	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:9598843-9600113	K562	blood:	n/a	n/a
16	POLR2A	chr1:9599162-9600693	IMR90	lung:	n/a	n/a
17	BACH1	chr1:9599134-9599634	H1-hESC	embryonic stem cell:	n/a	n/a
18	CREB1	chr1:9599079-9599760	K562	blood:	n/a	chr1:9599472-9599485
19	MXI1	chr1:9599136-9600435	GM12878	blood:	n/a	chr1:9599497-9599506
20	SIN3AK20	chr1:9599120-9599777	SK-N-SH	brain:	n/a	n/a
21	CHD2	chr1:9599049-9599568	HepG2	liver:	n/a	chr1:9599449-9599459
22	SP1	chr1:9598899-9599648	HCT-116	colon:	n/a	chr1:9599363-9599372 chr1:9599407-9599428 chr1:9599386-9599397 chr1:9599386-9599398 chr1:9599362-9599373 chr1:9599450-9599459 chr1:9599387-9599401 chr1:9599451-9599464 chr1:9599449-9599461 chr1:9599388-9599397 chr1:9599450-9599460 chr1:9599434-9599444 chr1:9599451-9599460 chr1:9599449-9599461 chr1:9599450-9599459
23	MAX	chr1:9598913-9600631	HCT-116	colon:	n/a	chr1:9599495-9599506 chr1:9599496-9599505 chr1:9599972-9599982 chr1:9599496-9599505 chr1:9599498-9599514 chr1:9599490-9599500 chr1:9599700-9599709
24	ZNF384	chr1:9599038-9599711	K562	blood:	n/a	n/a
25	REST	chr1:9599091-9599551	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr1:9599065-9600021	GM12878	blood:	n/a	n/a
27	JUND	chr1:9598868-9599698	K562	blood:	n/a	chr1:9599153-9599161 chr1:9599474-9599483
28	CEBPD	chr1:9598849-9599624	K562	blood:	n/a	n/a
29	POLR2A	chr1:9599047-9600489	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr1:9598966-9599756	A549	lung:	n/a	chr1:9599495-9599506 chr1:9599496-9599505 chr1:9599496-9599505 chr1:9599498-9599514 chr1:9599490-9599500 chr1:9599700-9599709
31	MAX	chr1:9598981-9599772	ECC-1	luminal epithelium:	n/a	chr1:9599495-9599506 chr1:9599496-9599505 chr1:9599496-9599505 chr1:9599498-9599514 chr1:9599490-9599500 chr1:9599700-9599709
32	POLR2A	chr1:9598946-9599950	GM12892	blood:	n/a	n/a
33	NFYB	chr1:9599144-9599543	K562	blood:	n/a	chr1:9599406-9599421 chr1:9599406-9599421 chr1:9599403-9599418 chr1:9599405-9599417 chr1:9599408-9599418 chr1:9599408-9599418 chr1:9599406-9599420
34	ELF1	chr1:9599142-9599655	HepG2	liver:	n/a	chr1:9599485-9599497 chr1:9599546-9599558 chr1:9599596-9599608
35	TAF7	chr1:9599106-9599793	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:9599002-9600183	HL-60	blood:	n/a	n/a
37	SP1	chr1:9599078-9599638	HepG2	liver:	n/a	chr1:9599363-9599372 chr1:9599407-9599428 chr1:9599386-9599397 chr1:9599386-9599398 chr1:9599362-9599373 chr1:9599450-9599459 chr1:9599387-9599401 chr1:9599451-9599464 chr1:9599449-9599461 chr1:9599388-9599397 chr1:9599450-9599460 chr1:9599434-9599444 chr1:9599451-9599460 chr1:9599449-9599461 chr1:9599450-9599459
38	POLR2A	chr1:9599041-9599688	SK-N-SH	brain:	n/a	n/a
39	REST	chr1:9598843-9599556	H1-neurons	neurons:	n/a	n/a
40	CHD2	chr1:9598186-9599600	K562	blood:	n/a	chr1:9599449-9599459
41	ELK4	chr1:9599169-9599573	Hela-S3	cervix:	n/a	n/a
42	SP1	chr1:9599046-9599666	A549	lung:	n/a	chr1:9599363-9599372 chr1:9599407-9599428 chr1:9599386-9599397 chr1:9599386-9599398 chr1:9599362-9599373 chr1:9599450-9599459 chr1:9599387-9599401 chr1:9599451-9599464 chr1:9599449-9599461 chr1:9599388-9599397 chr1:9599450-9599460 chr1:9599434-9599444 chr1:9599451-9599460 chr1:9599449-9599461 chr1:9599450-9599459
43	POLR2A	chr1:9597858-9600451	Raji	blood:	n/a	n/a
44	E2F6	chr1:9598946-9599694	A549	lung:	n/a	chr1:9599473-9599482 chr1:9599475-9599484
45	JUN	chr1:9598278-9600423	K562	blood:	n/a	chr1:9599153-9599161 chr1:9600138-9600147 chr1:9599474-9599483
46	POLR2A	chr1:9598837-9600558	K562	blood:	n/a	n/a
47	SIN3AK20	chr1:9599119-9600529	PANC-1	pancreas:	n/a	n/a
48	BRCA1	chr1:9599088-9599644	Hela-S3	cervix:	n/a	n/a
49	GTF2F1	chr1:9599115-9599453	Hela-S3	cervix:	n/a	n/a
50	HCFC1	chr1:9598952-9599904	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9597937..9599836-chr1:9648693..9652829,4	K562	blood:
2	chr1:9597781..9602686-chr1:9646599..9652829,9	K562	blood:
3	chr1:9597734..9599433-chr1:9617661..9619736,2	K562	blood:
4	chr1:9586876..9589181-chr1:9596662..9599409,2	K562	blood:
5	chr1:9599090..9600004-chr11:94964653..94965231,2	NB4	blood:
6	chr1:9294638..9296253-chr1:9598479..9600330,2	K562	blood:
7	chr1:9350586..9353918-chr1:9597167..9600975,3	MCF-7	breast:

Variant related genes	Relation type
SLC25A33	TF binding region
ENSG00000049239	Chromatin interaction
ENSG00000245552	Chromatin interaction
ENSG00000188807	Chromatin interaction
ENSG00000171621	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10159413	1.00[AMR][1000 genomes]
rs11121428	1.00[EUR][1000 genomes]
rs11804156	0.83[AFR][1000 genomes]
rs11811820	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066330	1.00[EUR][1000 genomes]
rs55913306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56133240	1.00[EUR][1000 genomes]
rs56133747	1.00[AMR][1000 genomes]
rs57585081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60678622	1.00[EUR][1000 genomes]
rs61547143	1.00[EUR][1000 genomes]
rs6701659	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72862732	1.00[EUR][1000 genomes]
rs72862734	1.00[EUR][1000 genomes]
rs7354926	1.00[EUR][1000 genomes]
rs74051506	1.00[AMR][1000 genomes]
rs74051508	1.00[AMR][1000 genomes]
rs74051509	1.00[AMR][1000 genomes]
rs74051510	1.00[AMR][1000 genomes]
rs74051513	1.00[AMR][1000 genomes]
rs74051531	1.00[EUR][1000 genomes]
rs74051533	1.00[EUR][1000 genomes]
rs74051544	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74051551	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74051552	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74051646	1.00[EUR][1000 genomes]
rs74051648	1.00[EUR][1000 genomes]
rs74051651	1.00[EUR][1000 genomes]
rs74051652	1.00[EUR][1000 genomes]
rs9662928	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	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS 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	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2476310	chr1:9593578-9600139	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv545377	chr1:9597237-9602962	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	esv3343289	chr1:9598765-9601013	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9555800-9599400	Weak transcription	Right Atrium	heart
2	chr1:9591600-9599400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:9593600-9599600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:9594400-9599400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:9596200-9599400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:9597200-9599200	Enhancers	Stomach Mucosa	stomach
7	chr1:9597800-9599200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:9597800-9599200	Flanking Active TSS	HepG2	liver
9	chr1:9597800-9599400	Enhancers	HMEC	breast
10	chr1:9597800-9599600	Enhancers	GM12878-XiMat	blood
11	chr1:9598000-9599200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:9598000-9599400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:9598000-9599400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:9598000-9599400	Enhancers	Brain Substantia Nigra	brain
15	chr1:9598000-9599400	Enhancers	Esophagus	oesophagus
16	chr1:9598000-9599400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:9598200-9599200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr1:9598200-9599200	Enhancers	Primary T cells from cord blood	blood
19	chr1:9598200-9599200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:9598200-9599200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:9598200-9599200	Enhancers	Spleen	Spleen
22	chr1:9598200-9599400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:9598200-9599400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:9598200-9599400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:9598200-9599400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:9598200-9599400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:9598200-9599400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:9598200-9599400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:9598200-9599400	Enhancers	Lung	lung
30	chr1:9598200-9599400	Enhancers	Pancreas	Pancrea
31	chr1:9598200-9599400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr1:9598200-9599600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr1:9598200-9599600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:9598200-9599800	Enhancers	Fetal Thymus	thymus
35	chr1:9598200-9600200	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:9598400-9599200	Enhancers	Primary B cells from cord blood	blood
37	chr1:9598400-9599200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:9598400-9599200	Flanking Active TSS	K562	blood
39	chr1:9598400-9599400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:9598400-9599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:9598400-9599600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:9598600-9599200	Flanking Active TSS	Colonic Mucosa	Colon
43	chr1:9598600-9599400	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:9598600-9599400	Enhancers	Small Intestine	intestine
45	chr1:9598800-9599200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:9598800-9599200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr1:9598800-9599200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr1:9598800-9599200	Enhancers	Brain Hippocampus Middle	brain
49	chr1:9598800-9599400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:9598800-9599400	Enhancers	Duodenum Smooth Muscle	Duodenum

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