Variant report

Variant	rs7181758
Chromosome Location	chr15:42564902-42564903
allele	A/C
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	KAP1	chr15:42564749-42566769	HEK293	kidney:	n/a	chr15:42566671-42566679
2	POLR2A	chr15:42564877-42566879	SK-N-MC	brain:	n/a	n/a
3	BRCA1	chr15:42564758-42566829	Hela-S3	cervix:	n/a	chr15:42565231-42565238
4	POLR2A	chr15:42564850-42566633	U87	brain:	n/a	n/a
5	POLR2A	chr15:42564858-42566890	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr15:42564606-42566670	GM12878	blood:	n/a	n/a
7	MXI1	chr15:42564709-42567069	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:42564894-42566771	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr15:42564676-42566871	IMR90	lung:	n/a	n/a
10	KAP1	chr15:42564813-42566201	U2OS	brain:	n/a	n/a
11	POLR2A	chr15:42564739-42566892	Hela-S3	cervix:	n/a	n/a
12	HCFC1	chr15:42564125-42567794	Hela-S3	cervix:	n/a	n/a
13	CHD1	chr15:42564623-42565634	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr15:42564199-42567248	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr15:42564870-42566689	PFSK-1	brain:	n/a	n/a
16	MAZ	chr15:42564671-42566752	IMR90	lung:	n/a	n/a
17	POLR2A	chr15:42564791-42566839	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:42564593-42567021	MCF10A-Er-Src	breast:	n/a	n/a
19	RAD21	chr15:42564697-42566036	IMR90	lung:	n/a	chr15:42565005-42565014
20	SMARCC1	chr15:42564666-42567115	Hela-S3	cervix:	n/a	n/a
21	MAZ	chr15:42564693-42566678	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr15:42564691-42566704	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr15:42564844-42566754	U87	brain:	n/a	n/a
24	POLR2A	chr15:42564823-42567120	PANC-1	pancreas:	n/a	n/a
25	STAT3	chr15:42564609-42566740	GM12878	blood:	n/a	chr15:42566553-42566564 chr15:42566555-42566563 chr15:42566398-42566409 chr15:42564745-42564753 chr15:42565052-42565063
26	MXI1	chr15:42564068-42568476	SK-N-SH	brain:	n/a	n/a
27	NRF1	chr15:42564874-42566114	SK-N-SH	brain:	n/a	chr15:42565779-42565793 chr15:42565782-42565791 chr15:42565781-42565792
28	RCOR1	chr15:42564607-42567069	Hela-S3	cervix:	n/a	n/a
29	MAFK	chr15:42564732-42565842	IMR90	lung:	n/a	chr15:42564736-42564747
30	MAFK	chr15:42564887-42567045	Hela-S3	cervix:	n/a	chr15:42566799-42566815 chr15:42566799-42566814 chr15:42566799-42566810 chr15:42566799-42566810
31	POLR2A	chr15:42564854-42567158	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42499099..42501734-chr15:42564008..42565710,2	K562	blood:
2	chr15:42564636..42566534-chr15:42781561..42783413,2	K562	blood:
3	chr15:42563158..42565885-chr15:42567865..42572400,4	MCF-7	breast:
4	chr15:42498938..42502268-chr15:42564432..42567193,3	MCF-7	breast:
5	chr15:42563255..42565132-chr15:42636659..42638368,2	K562	blood:

Variant related genes	Relation type
GANC	TF binding region
TMEM87A	TF binding region
ENSG00000261002	Chromatin interaction
ENSG00000214013	Chromatin interaction
ENSG00000166887	Chromatin interaction
ENSG00000103994	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11070371	1.00[AMR][1000 genomes]
rs11633276	1.00[AMR][1000 genomes]
rs1659216	1.00[AMR][1000 genomes]
rs1659225	1.00[AMR][1000 genomes]
rs2289297	1.00[AMR][1000 genomes]
rs2412689	1.00[AMR][1000 genomes]
rs2578651	1.00[AMR][1000 genomes]
rs28364398	1.00[AMR][1000 genomes]
rs28364400	1.00[AMR][1000 genomes]
rs28364503	1.00[AMR][1000 genomes]
rs28364507	1.00[AMR][1000 genomes]
rs28364557	1.00[AMR][1000 genomes]
rs28489155	1.00[AMR][1000 genomes]
rs28621687	1.00[AMR][1000 genomes]
rs4923939	1.00[AMR][1000 genomes]
rs4924657	1.00[AMR][1000 genomes]
rs595661	1.00[AMR][1000 genomes]
rs6493031	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs655704	1.00[AMR][1000 genomes]
rs685447	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7161982	1.00[AMR][1000 genomes]
rs7177193	1.00[AMR][1000 genomes]
rs936603	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr15:42552600-42565000	Weak transcription	Gastric	stomach
2	chr15:42552600-42565200	Weak transcription	Spleen	Spleen
3	chr15:42556000-42565000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:42562800-42565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:42562800-42565000	Weak transcription	Pancreas	Pancrea
6	chr15:42562800-42566600	Active TSS	NHLF	lung
7	chr15:42563000-42566800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:42563000-42566800	Active TSS	Fetal Intestine Large	intestine
9	chr15:42563200-42567400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:42563400-42566400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:42563400-42566600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:42563400-42568200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:42563400-42568600	Active TSS	Right Atrium	heart
14	chr15:42563600-42566800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:42563600-42566800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:42563800-42566600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:42563800-42566600	Active TSS	HMEC	breast
18	chr15:42563800-42567000	Active TSS	GM12878-XiMat	blood
19	chr15:42564000-42565800	Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:42564000-42565800	Active TSS	NH-A	brain
21	chr15:42564000-42566400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr15:42564000-42566600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:42564000-42566600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:42564000-42566600	Active TSS	Brain Germinal Matrix	brain
25	chr15:42564000-42566600	Active TSS	NHEK	skin
26	chr15:42564000-42566800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:42564000-42566800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr15:42564000-42566800	Active TSS	NHDF-Ad	bronchial
29	chr15:42564000-42567000	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr15:42564000-42567200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:42564000-42567600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr15:42564000-42568400	Active TSS	K562	blood
33	chr15:42564200-42565000	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr15:42564200-42565000	Flanking Active TSS	Dnd41	blood
35	chr15:42564200-42565200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:42564200-42566600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:42564200-42566800	Active TSS	Fetal Kidney	kidney
38	chr15:42564200-42567000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr15:42564200-42567000	Active TSS	A549	lung
40	chr15:42564400-42565000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr15:42564400-42565000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:42564400-42565000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr15:42564400-42565000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr15:42564400-42565000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr15:42564400-42565000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:42564400-42565000	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr15:42564400-42565000	Flanking Active TSS	Liver	Liver
48	chr15:42564400-42565000	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr15:42564400-42565000	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr15:42564400-42565000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links