Variant report

Variant	rs45551532
Chromosome Location	chr6:49518599-49518600
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	MAX	chr6:49517755-49519554	HCT-116	colon:	n/a	chr6:49518356-49518363
2	MAX	chr6:49517644-49519344	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
3	POLR2A	chr6:49517816-49519779	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr6:49517756-49519681	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:49518165-49518710	ProgFib	skin:	n/a	n/a
6	TAF1	chr6:49517776-49518762	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF2	chr6:49518196-49518625	H1-hESC	embryonic stem cell:	n/a	n/a
8	PML	chr6:49517953-49518719	MCF-7	breast:	n/a	n/a
9	HA-E2F1	chr6:49517738-49519388	MCF-7	breast:	n/a	n/a
10	TAF1	chr6:49518002-49518800	MCF-7	breast:	n/a	n/a
11	E2F6	chr6:49518255-49518629	A549	lung:	n/a	n/a
12	CHD1	chr6:49517877-49518628	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr6:49518049-49519231	MCF-7	breast:	n/a	chr6:49518356-49518363
14	SIN3A	chr6:49517827-49519792	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF263	chr6:49517770-49519815	HEK293-T-REx	kidney:	n/a	chr6:49518987-49519008
16	POLR2A	chr6:49518013-49518676	HCT-116	colon:	n/a	n/a
17	TAF1	chr6:49518073-49518736	A549	lung:	n/a	n/a
18	E2F6	chr6:49517622-49519321	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:49517913-49518611	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:49518067-49518661	HUVEC	blood vessel:	n/a	n/a
21	MAX	chr6:49518137-49519242	ECC-1	luminal epithelium:	n/a	chr6:49518356-49518363
22	CTBP2	chr6:49517789-49519491	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:49518015-49518672	U87	brain:	n/a	n/a
24	MAX	chr6:49518152-49518993	A549	lung:	n/a	chr6:49518356-49518363
25	MAX	chr6:49517624-49519414	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
26	ZNF143	chr6:49517701-49519549	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr6:49517734-49519487	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
28	MAX	chr6:49517923-49518755	HCT-116	colon:	n/a	chr6:49518356-49518363
29	JUND	chr6:49517854-49518883	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr6:49518036-49519301	A549	lung:	n/a	chr6:49518356-49518363
31	POLR2A	chr6:49517634-49519474	H1-hESC	embryonic stem cell:	n/a	n/a
32	ELF1	chr6:49518099-49518605	MCF-7	breast:	n/a	n/a
33	E2F6	chr6:49517510-49519567	H1-hESC	embryonic stem cell:	n/a	n/a
34	E2F6	chr6:49518038-49519263	A549	lung:	n/a	n/a
35	MAX	chr6:49517887-49519342	A549	lung:	n/a	chr6:49518356-49518363
36	POLR2A	chr6:49517623-49519307	MCF-7	breast:	n/a	n/a
37	POLR2A	chr6:49518594-49519186	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr6:49518164-49519126	A549	lung:	n/a	n/a
39	CHD2	chr6:49517847-49519023	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr6:49518010-49518646	SK-N-MC	brain:	n/a	n/a
41	HDAC2	chr6:49518101-49518607	MCF-7	breast:	n/a	n/a
42	TAF1	chr6:49517711-49519429	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:49518254-49518705	A549	lung:	n/a	n/a
44	POLR2A	chr6:49517622-49519547	H1-hESC	embryonic stem cell:	n/a	n/a
45	SIN3AK20	chr6:49517764-49519402	MCF-7	breast:	n/a	n/a
46	TAF1	chr6:49517925-49518733	MCF-7	breast:	n/a	n/a
47	TCF12	chr6:49517897-49519335	A549	lung:	n/a	n/a
48	GTF2F1	chr6:49517829-49519427	H1-hESC	embryonic stem cell:	n/a	n/a
49	GATA3	chr6:49518086-49518611	MCF-7	breast:	n/a	n/a
50	SIN3AK20	chr6:49517749-49519895	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49429390..49432411-chr6:49516710..49519961,3	MCF-7	breast:

Variant related genes	Relation type
C6orf141	TF binding region
ENSG00000146085	Chromatin interaction
ENSG00000031691	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10456625	1.00[EUR][1000 genomes]
rs41273692	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458697	1.00[EUR][1000 genomes]
rs6905369	1.00[EUR][1000 genomes]
rs6912159	1.00[EUR][1000 genomes]
rs6912178	1.00[EUR][1000 genomes]
rs6912690	1.00[EUR][1000 genomes]
rs6919458	1.00[EUR][1000 genomes]
rs6925445	1.00[EUR][1000 genomes]
rs6927176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6927459	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6939453	1.00[EUR][1000 genomes]
rs6939457	1.00[EUR][1000 genomes]
rs73431965	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73431999	1.00[EUR][1000 genomes]
rs73433806	1.00[EUR][1000 genomes]
rs73433809	1.00[EUR][1000 genomes]
rs73433816	1.00[EUR][1000 genomes]
rs7742891	1.00[EUR][1000 genomes]
rs7758141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760893	1.00[EUR][1000 genomes]
rs7761036	1.00[EUR][1000 genomes]
rs7761928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9349495	1.00[EUR][1000 genomes]
rs9473590	1.00[EUR][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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49517400-49519800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:49517400-49520000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr6:49517400-49520000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:49517600-49519800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr6:49517800-49518800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:49517800-49518800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr6:49517800-49519000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:49517800-49519000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:49517800-49519000	Active TSS	Brain Anterior Caudate	brain
10	chr6:49517800-49519200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
11	chr6:49517800-49519400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:49517800-49519400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:49517800-49519600	Active TSS	Rectal Smooth Muscle	rectum
14	chr6:49517800-49519800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:49517800-49520200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:49517800-49520200	Active TSS	A549	lung
17	chr6:49518000-49518600	Flanking Active TSS	Placenta	Placenta
18	chr6:49518000-49518600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:49518000-49518800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr6:49518000-49518800	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:49518000-49518800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:49518000-49518800	Active TSS	Esophagus	oesophagus
23	chr6:49518000-49518800	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr6:49518000-49519000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:49518000-49519000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr6:49518000-49519000	Active TSS	Gastric	stomach
27	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
28	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:49518000-49519200	Flanking Active TSS	Pancreas	Pancrea
32	chr6:49518000-49519200	Bivalent/Poised TSS	Stomach Mucosa	stomach
33	chr6:49518000-49519400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:49518000-49519400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
36	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
37	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
40	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
41	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
42	chr6:49518000-49519400	Enhancers	Spleen	Spleen
43	chr6:49518000-49519400	Bivalent/Poised TSS	HSMM	muscle
44	chr6:49518000-49519600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
45	chr6:49518000-49519600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
46	chr6:49518000-49519600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr6:49518000-49519600	Bivalent/Poised TSS	Fetal Brain Female	brain
48	chr6:49518000-49519600	Bivalent/Poised TSS	Fetal Kidney	kidney
49	chr6:49518000-49519600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr6:49518000-49519800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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