Variant report

Variant	rs41273692
Chromosome Location	chr6:49519169-49519170
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	HDAC2	chr6:49519129-49519470	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:49518693-49519494	H1-hESC	embryonic stem cell:	n/a	n/a
7	HA-E2F1	chr6:49517738-49519388	MCF-7	breast:	n/a	n/a
8	MAX	chr6:49518049-49519231	MCF-7	breast:	n/a	chr6:49518356-49518363
9	BACH1	chr6:49518765-49519444	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr6:49517827-49519792	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF263	chr6:49517770-49519815	HEK293-T-REx	kidney:	n/a	chr6:49518987-49519008
12	E2F6	chr6:49517622-49519321	H1-hESC	embryonic stem cell:	n/a	n/a
13	EBF1	chr6:49519052-49519304	GM12878	blood:	n/a	chr6:49519203-49519214
14	SP1	chr6:49519142-49519678	H1-hESC	embryonic stem cell:	n/a	chr6:49519565-49519577 chr6:49519566-49519575 chr6:49519566-49519575 chr6:49519567-49519576 chr6:49519566-49519580
15	JUND	chr6:49519096-49519493	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr6:49518137-49519242	ECC-1	luminal epithelium:	n/a	chr6:49518356-49518363
17	CTBP2	chr6:49517789-49519491	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:49518911-49519538	H1-neurons	neurons:	n/a	n/a
19	CHD1	chr6:49518945-49519340	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr6:49517624-49519414	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
21	ZNF143	chr6:49517701-49519549	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr6:49517734-49519487	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
23	MAX	chr6:49518036-49519301	A549	lung:	n/a	chr6:49518356-49518363
24	POLR2A	chr6:49517634-49519474	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr6:49517510-49519567	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F6	chr6:49518038-49519263	A549	lung:	n/a	n/a
27	MAX	chr6:49517887-49519342	A549	lung:	n/a	chr6:49518356-49518363
28	POLR2A	chr6:49517623-49519307	MCF-7	breast:	n/a	n/a
29	POLR2A	chr6:49518594-49519186	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr6:49518775-49519481	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr6:49519089-49519267	MCF10A-Er-Src	breast:	n/a	n/a
32	TAF1	chr6:49517711-49519429	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:49518843-49519197	HCT-116	colon:	n/a	n/a
34	POLR2A	chr6:49517622-49519547	H1-hESC	embryonic stem cell:	n/a	n/a
35	SIN3AK20	chr6:49517764-49519402	MCF-7	breast:	n/a	n/a
36	TCF12	chr6:49517897-49519335	A549	lung:	n/a	n/a
37	GTF2F1	chr6:49517829-49519427	H1-hESC	embryonic stem cell:	n/a	n/a
38	SIN3AK20	chr6:49517749-49519895	MCF-7	breast:	n/a	n/a
39	TBP	chr6:49517734-49519568	H1-hESC	embryonic stem cell:	n/a	n/a
40	USF2	chr6:49518876-49519468	H1-hESC	embryonic stem cell:	n/a	n/a
41	NANOG	chr6:49519049-49519547	H1-hESC	embryonic stem cell:	n/a	chr6:49519525-49519534
42	MYC	chr6:49518527-49519186	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:49519099-49519454	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr6:49518019-49519557	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr6:49517983-49519354	MCF-7	breast:	n/a	n/a
46	POLR2A	chr6:49517808-49519323	MCF-7	breast:	n/a	n/a
47	KAP1	chr6:49517941-49519534	HEK293	kidney:	n/a	n/a
48	TEAD4	chr6:49519168-49519637	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr6:49519100-49519250	BE2_C	brain:	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
ENSG00000031691	Chromatin interaction
ENSG00000146085	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]
rs41273694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45551532	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6927459	1.00[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	0.95[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	1.00[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	1.00[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:122 , 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	chr6:49517800-49519200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
6	chr6:49517800-49519400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:49517800-49519400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:49517800-49519600	Active TSS	Rectal Smooth Muscle	rectum
9	chr6:49517800-49519800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:49517800-49520200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:49517800-49520200	Active TSS	A549	lung
12	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
13	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:49518000-49519200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:49518000-49519200	Flanking Active TSS	Pancreas	Pancrea
17	chr6:49518000-49519200	Bivalent/Poised TSS	Stomach Mucosa	stomach
18	chr6:49518000-49519400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:49518000-49519400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
21	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
25	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
26	chr6:49518000-49519400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
27	chr6:49518000-49519400	Enhancers	Spleen	Spleen
28	chr6:49518000-49519400	Bivalent/Poised TSS	HSMM	muscle
29	chr6:49518000-49519600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
30	chr6:49518000-49519600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
31	chr6:49518000-49519600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr6:49518000-49519600	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr6:49518000-49519600	Bivalent/Poised TSS	Fetal Kidney	kidney
34	chr6:49518000-49519600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr6:49518000-49519800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:49518000-49519800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:49518000-49519800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:49518000-49519800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr6:49518000-49519800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:49518000-49519800	Flanking Active TSS	Liver	Liver
41	chr6:49518000-49519800	Bivalent/Poised TSS	NHDF-Ad	bronchial
42	chr6:49518000-49520000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr6:49518000-49520200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:49518000-49520200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr6:49518000-49520600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:49518000-49520600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:49518200-49519200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
48	chr6:49518200-49519200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:49518200-49519200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:49518200-49519200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain

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