Variant report

Variant	rs413842
Chromosome Location	chr6:75917523-75917524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr6:75913908-75917770	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:75917440-75917570	MCF-7	breast:	n/a	n/a
3	TEAD4	chr6:75917141-75917542	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr6:75917350-75917628	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:75917513-75917536	MCF-7	breast:	n/a	n/a
6	CTCF	chr6:75917520-75917670	RPTEC	kidney:	n/a	n/a
7	ZNF143	chr6:75917440-75917679	H1-hESC	embryonic stem cell:	n/a	n/a
8	SUZ12	chr6:75913870-75918221	NT2-D1	testis:	n/a	n/a
9	POLR2A	chr6:75916748-75917814	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr6:75917454-75918172	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:75914858-75917612	H1-neurons	neurons:	n/a	n/a
12	TBP	chr6:75916619-75917804	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTBP2	chr6:75914069-75917676	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr6:75917232-75917701	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3A	chr6:75917110-75918956	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74229352..74231539-chr6:75915151..75917818,2	MCF-7	breast:
2	chr6:74495117..74497243-chr6:75916088..75918968,2	MCF-7	breast:
3	chr6:75915774..75918712-chr6:75944046..75945609,2	MCF-7	breast:

No data

Variant related genes	Relation type
COL12A1	TF binding region
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11965620	1.00[AMR][1000 genomes]
rs171265	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240435	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2951927	1.00[AMR][1000 genomes]
rs2998377	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022377	chr6:75762463-75919592	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv538309	chr6:75762463-75919592	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv886181	chr6:75852488-75919484	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75913000-75918400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr6:75913600-75918400	Active TSS	Rectal Smooth Muscle	rectum
3	chr6:75913800-75917600	Active TSS	Placenta Amnion	Placenta Amnion
4	chr6:75913800-75918000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:75913800-75918400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:75913800-75918600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:75913800-75918800	Active TSS	Right Atrium	heart
8	chr6:75914000-75918800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:75914200-75917800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:75914200-75917800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
11	chr6:75914200-75918200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr6:75914200-75918800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:75914400-75917800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
14	chr6:75914400-75917800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
15	chr6:75914400-75917800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
16	chr6:75914400-75917800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr6:75914400-75918400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:75914600-75917800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:75914800-75918400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:75914800-75918800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr6:75915000-75918200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
22	chr6:75915200-75918400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr6:75915600-75918200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:75915800-75917800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
25	chr6:75915800-75918800	Bivalent Enhancer	Placenta	Placenta
26	chr6:75916000-75917800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:75916000-75918200	Bivalent Enhancer	Primary B cells from cord blood	blood
28	chr6:75916000-75918200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr6:75916000-75918200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr6:75916000-75918600	Bivalent Enhancer	Liver	Liver
31	chr6:75916000-75918600	Enhancers	Gastric	stomach
32	chr6:75916000-75918600	Enhancers	Spleen	Spleen
33	chr6:75916200-75918000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:75916400-75917600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:75916400-75918400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr6:75916400-75918400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:75916400-75918400	Weak transcription	A549	lung
38	chr6:75916400-75918400	Weak transcription	HSMM	muscle
39	chr6:75916400-75918400	Weak transcription	HSMMtube	muscle
40	chr6:75916600-75917600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:75916600-75917600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:75916600-75917800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:75916600-75917800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:75916600-75917800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:75916600-75917800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:75916600-75918000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:75916600-75918000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:75916600-75918400	Weak transcription	Aorta	Aorta
49	chr6:75916600-75918400	Weak transcription	Ovary	ovary
50	chr6:75916600-75918800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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