Variant report

Variant	rs73739170
Chromosome Location	chr6:27561249-27561250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27559682-27561420	H1-neurons	neurons:	n/a	n/a
2	SIN3A	chr6:27559517-27561282	H1-hESC	embryonic stem cell:	n/a	chr6:27561096-27561109
3	TEAD4	chr6:27559243-27561438	K562	blood:	n/a	n/a
4	ZMIZ1	chr6:27561174-27561329	K562	blood:	n/a	n/a
5	POLR2A	chr6:27559692-27561541	H1-neurons	neurons:	n/a	n/a
6	CBX3	chr6:27559260-27561263	K562	blood:	n/a	n/a
7	RCOR1	chr6:27560307-27561269	K562	blood:	n/a	n/a
8	TBL1XR1	chr6:27561190-27561366	K562	blood:	n/a	n/a
9	SREBP2	chr6:27559251-27561607	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27520903..27523878-chr6:27561222..27562746,2	MCF-7	breast:
2	chr6:27561158..27562772-chr6:27575772..27577802,2	K562	blood:
3	chr6:27558513..27562026-chr6:27562388..27564787,3	K562	blood:
4	chr6:27531650..27535233-chr6:27560375..27562860,3	K562	blood:
5	chr6:27532623..27535233-chr6:27560375..27562747,2	K562	blood:
6	chr6:27516649..27519121-chr6:27558606..27561383,2	K562	blood:
7	chr6:27549818..27556949-chr6:27557615..27563432,7	K562	blood:
8	chr6:27549715..27554180-chr6:27555593..27563261,8	K562	blood:
9	chr6:27560791..27564329-chr6:27775763..27778725,3	K562	blood:
10	chr6:27560152..27562900-chr6:28715549..28717321,2	K562	blood:
11	chr6:27558513..27561961-chr6:27562522..27566444,4	K562	blood:
12	chr6:27484948..27487282-chr6:27561197..27562747,2	K562	blood:

No data

Variant related genes	Relation type
RNU6-471P	TF binding region
ENSG00000206671	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs56300543	0.90[AFR][1000 genomes]
rs57451619	0.85[AFR][1000 genomes]
rs58103199	0.90[AFR][1000 genomes]
rs58176220	1.00[AFR][1000 genomes]
rs58581731	1.00[AFR][1000 genomes]
rs59760836	0.90[AFR][1000 genomes]
rs60226202	0.90[AFR][1000 genomes]
rs61471498	0.80[AFR][1000 genomes]
rs73739108	0.90[AFR][1000 genomes]
rs73739109	0.90[AFR][1000 genomes]
rs73739123	0.90[AFR][1000 genomes]
rs73739134	0.90[AFR][1000 genomes]
rs73739136	0.90[AFR][1000 genomes]
rs73739138	0.90[AFR][1000 genomes]
rs73739147	0.90[AFR][1000 genomes]
rs73739148	1.00[AFR][1000 genomes]
rs73739149	0.90[AFR][1000 genomes]
rs73739152	0.90[AFR][1000 genomes]
rs73739153	0.90[AFR][1000 genomes]
rs73739155	0.90[AFR][1000 genomes]
rs73739171	0.90[AFR][1000 genomes]
rs73739173	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27559600-27561400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:27559600-27561400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27559600-27561400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:27559600-27561600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr6:27559600-27561600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:27559600-27561800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:27559600-27562000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:27559600-27562200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:27559600-27562200	Active TSS	A549	lung
10	chr6:27559600-27562600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:27559600-27562800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:27559800-27561400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:27559800-27561400	Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:27559800-27561400	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr6:27559800-27561400	Active TSS	NHLF	lung
16	chr6:27559800-27561600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:27559800-27561800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:27559800-27562000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr6:27560000-27561400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
20	chr6:27560600-27561400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:27560600-27561400	Flanking Active TSS	NHEK	skin
22	chr6:27560600-27561600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:27560800-27561400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:27560800-27561400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:27560800-27561400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:27560800-27561400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr6:27560800-27561400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
28	chr6:27560800-27561400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr6:27560800-27561400	Bivalent Enhancer	Fetal Heart	heart
30	chr6:27560800-27561600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
31	chr6:27560800-27561800	Flanking Active TSS	HMEC	breast
32	chr6:27560800-27562000	Flanking Active TSS	K562	blood
33	chr6:27560800-27562400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr6:27560800-27562600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:27560800-27562800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:27560800-27563000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr6:27560800-27563000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr6:27560800-27563000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:27560800-27563000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:27561000-27561400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:27561000-27561400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:27561000-27561400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:27561000-27561400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
44	chr6:27561000-27561400	Bivalent Enhancer	Esophagus	oesophagus
45	chr6:27561000-27561400	ZNF genes & repeats	Spleen	Spleen
46	chr6:27561000-27561400	Bivalent/Poised TSS	HSMM	muscle
47	chr6:27561000-27561400	Bivalent/Poised TSS	NHDF-Ad	bronchial
48	chr6:27561000-27561400	Flanking Bivalent TSS/Enh	Osteobl	bone
49	chr6:27561000-27561600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:27561000-27561600	Bivalent/Poised TSS	NH-A	brain

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