Variant report

Variant	rs6457741
Chromosome Location	chr6:33756026-33756027
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	RUNX3	chr6:33755653-33756340	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:33754660-33756447	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr6:33755871-33757080	K562	blood:	n/a	n/a
4	YY1	chr6:33755711-33757699	SK-N-SH	brain:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
5	TCF12	chr6:33755925-33757295	ECC-1	luminal epithelium:	n/a	n/a
6	MAZ	chr6:33754791-33757409	IMR90	lung:	n/a	chr6:33756978-33756987
7	POLR2A	chr6:33755036-33756338	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr6:33756000-33756150	GM12868	blood:	n/a	n/a
9	CHD1	chr6:33753489-33757327	IMR90	lung:	n/a	n/a
10	POLR2A	chr6:33754637-33757242	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr6:33755375-33757546	GM12878	blood:	n/a	n/a
12	ELK1	chr6:33755973-33756232	Hela-S3	cervix:	n/a	chr6:33756062-33756071 chr6:33756062-33756071
13	POLR2A	chr6:33755859-33756325	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:33754307-33756475	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr6:33755770-33756323	H1-neurons	neurons:	n/a	n/a
16	MAX	chr6:33755863-33756433	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr6:33755402-33757555	GM12892	blood:	n/a	n/a
18	SIX5	chr6:33755981-33756180	A549	lung:	n/a	n/a
19	FOXA1	chr6:33755490-33756178	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:33755726-33757121	HepG2	liver:	n/a	n/a
21	ELF1	chr6:33755907-33756265	A549	lung:	n/a	n/a
22	RUNX3	chr6:33755605-33756281	GM12878	blood:	n/a	n/a
23	TBP	chr6:33755702-33756238	H1-hESC	embryonic stem cell:	n/a	n/a
24	GABPA	chr6:33755631-33756323	MCF-7	breast:	n/a	chr6:33756135-33756149 chr6:33756138-33756152
25	GABPA	chr6:33755787-33756308	A549	lung:	n/a	chr6:33756135-33756149 chr6:33756138-33756152
26	POLR2A	chr6:33755554-33756478	GM12892	blood:	n/a	n/a
27	YY1	chr6:33755901-33756188	K562	blood:	n/a	chr6:33756132-33756143
28	MAX	chr6:33755894-33756295	NB4	blood:	n/a	n/a
29	POLR2A	chr6:33755608-33757706	HL-60	blood:	n/a	n/a
30	POLR2A	chr6:33754123-33757999	HUVEC	blood vessel:	n/a	n/a
31	HMGN3	chr6:33755984-33757164	K562	blood:	n/a	n/a
32	YY1	chr6:33755721-33756268	SK-N-SH_RA	brain:	n/a	chr6:33756132-33756143
33	BHLHE40	chr6:33755790-33756195	GM12878	blood:	n/a	n/a
34	GATA2	chr6:33755336-33756232	HUVEC	blood vessel:	n/a	chr6:33755580-33755593 chr6:33755582-33755591
35	MXI1	chr6:33755951-33757227	HepG2	liver:	n/a	n/a
36	MYC	chr6:33755944-33756200	HepG2	liver:	n/a	n/a
37	ETS1	chr6:33755754-33756229	GM12878	blood:	n/a	chr6:33756062-33756071 chr6:33756062-33756071 chr6:33756062-33756071 chr6:33756063-33756073 chr6:33756059-33756074 chr6:33756062-33756071 chr6:33756058-33756074 chr6:33756062-33756071 chr6:33756062-33756073
38	MAX	chr6:33755692-33757692	HepG2	liver:	n/a	chr6:33756978-33756987
39	POLR2A	chr6:33754585-33758231	HepG2	liver:	n/a	n/a
40	ZNF263	chr6:33755920-33757230	HEK293-T-REx	kidney:	n/a	n/a
41	USF1	chr6:33755897-33756207	SK-N-SH_RA	brain:	n/a	n/a
42	SPI1	chr6:33755697-33756126	HL-60	blood:	n/a	chr6:33755847-33755854
43	POLR2A	chr6:33755761-33756375	SK-N-SH	brain:	n/a	n/a
44	YY1	chr6:33755941-33757702	K562	blood:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
45	STAT1	chr6:33755904-33756223	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:33755797-33756438	MCF-7	breast:	n/a	n/a
47	POLR2A	chr6:33755828-33756355	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr6:33755903-33756236	GM12878	blood:	n/a	n/a
49	ELF1	chr6:33755695-33757292	GM12878	blood:	n/a	n/a
50	HCFC1	chr6:33755934-33757398	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33677680..33679812-chr6:33755384..33758328,2	MCF-7	breast:
2	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
3	chr6:33755468..33757115-chr6:34205033..34207556,2	MCF-7	breast:
4	chr6:33754851..33757425-chr6:33862551..33864997,3	MCF-7	breast:
5	chr6:33743352..33745913-chr6:33755354..33756938,3	MCF-7	breast:
6	chr6:33678014..33680671-chr6:33755515..33757218,2	K562	blood:
7	chr17:48943386..48944014-chr6:33755667..33756340,2	Hela-S3	cervix:
8	chr6:33550386..33552584-chr6:33755194..33756833,2	MCF-7	breast:
9	chr6:33755622..33756350-chr7:25164616..25165317,2	Hela-S3	cervix:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000141232	Chromatin interaction
ENSG00000204188	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000161904	Chromatin interaction
ENSG00000249346	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000172115	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12173787	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12190029	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2013365	0.90[AFR][1000 genomes]
rs2281820	0.90[EUR][1000 genomes]
rs2296744	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2296746	0.81[AFR][1000 genomes]
rs2296747	0.93[AFR][1000 genomes]
rs2296748	0.81[AFR][1000 genomes]
rs2395402	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711347	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711348	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711349	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713678	0.81[EUR][1000 genomes]
rs4713679	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713681	0.93[AFR][1000 genomes]
rs6922275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747694	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751728	0.88[AFR][1000 genomes]
rs7774620	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380378	0.89[AFR][1000 genomes]
rs9394166	0.81[AFR][1000 genomes]
rs9394167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943471	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription 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	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33754200-33756400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr6:33754400-33756200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:33754400-33756200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:33754800-33756200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:33754800-33756200	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr6:33755000-33756200	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr6:33755000-33756200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:33755200-33756200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:33755200-33756200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:33755200-33756200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:33755200-33756200	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr6:33755200-33756200	Flanking Active TSS	Fetal Brain Male	brain
13	chr6:33755200-33756200	Flanking Active TSS	Fetal Brain Female	brain
14	chr6:33755400-33756200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr6:33755400-33756200	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr6:33755400-33756200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr6:33755400-33756200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr6:33755400-33756600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:33755400-33757000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:33755600-33756200	Active TSS	Right Atrium	heart
21	chr6:33755600-33757000	Active TSS	Ovary	ovary
22	chr6:33755600-33757200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr6:33755600-33757400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:33755800-33756200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr6:33755800-33756200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:33755800-33756200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
27	chr6:33755800-33756400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:33755800-33757000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:33755800-33757000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:33755800-33757000	Active TSS	Aorta	Aorta
31	chr6:33755800-33757000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr6:33755800-33757000	Active TSS	Fetal Kidney	kidney
33	chr6:33755800-33757000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:33755800-33757000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr6:33755800-33757000	Active TSS	Small Intestine	intestine
36	chr6:33755800-33757000	Active TSS	HepG2	liver
37	chr6:33755800-33757200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:33755800-33757200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr6:33755800-33757200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:33755800-33757200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr6:33755800-33757200	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr6:33755800-33757200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:33755800-33757200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:33755800-33757200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:33755800-33757200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:33755800-33757200	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:33755800-33757200	Active TSS	Fetal Intestine Large	intestine
48	chr6:33755800-33757200	Active TSS	Fetal Intestine Small	intestine
49	chr6:33755800-33757200	Active TSS	Left Ventricle	heart
50	chr6:33755800-33757200	Active TSS	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links