Variant report

Variant	rs559298138
Chromosome Location	chr13:110440052-110440053
allele	C/G
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	MXI1	chr13:110431145-110440503	SK-N-SH	brain:	n/a	chr13:110439837-110439852 chr13:110440136-110440145
2	MXI1	chr13:110436490-110440190	IMR90	lung:	n/a	chr13:110439837-110439852 chr13:110440136-110440145
3	MYC	chr13:110440045-110440216	MCF-7	breast:	n/a	n/a
4	MAZ	chr13:110437525-110440521	IMR90	lung:	n/a	chr13:110439018-110439028 chr13:110439313-110439323
5	POLR2A	chr13:110438646-110440459	HL-60	blood:	n/a	n/a
6	ZBTB7A	chr13:110439091-110440310	ECC-1	luminal epithelium:	n/a	chr13:110439693-110439702 chr13:110439264-110439271
7	POLR2A	chr13:110438737-110440281	U87	brain:	n/a	n/a
8	TAF1	chr13:110437993-110440294	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr13:110438701-110440287	K562	blood:	n/a	chr13:110438970-110438980 chr13:110439018-110439028 chr13:110439313-110439323
10	POLR2A	chr13:110436486-110440423	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr13:110439143-110440245	A549	lung:	n/a	n/a
12	REST	chr13:110437289-110440346	H1-neurons	neurons:	n/a	chr13:110439012-110439025 chr13:110439607-110439620 chr13:110439846-110439859
13	CTCF	chr13:110439960-110440110	HMEC	breast:	n/a	n/a
14	SIN3A	chr13:110438551-110440365	H1-hESC	embryonic stem cell:	n/a	chr13:110439607-110439620 chr13:110438565-110438578 chr13:110439579-110439590
15	POLR2A	chr13:110431400-110440383	NB4	blood:	n/a	n/a
16	POLR2A	chr13:110429835-110441120	MCF10A-Er-Src	breast:	n/a	n/a
17	ZBTB7A	chr13:110439368-110440198	K562	blood:	n/a	chr13:110439693-110439702
18	SMC3	chr13:110438759-110440350	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr13:110431377-110440356	Hela-S3	cervix:	n/a	n/a
20	GTF2F1	chr13:110439983-110440062	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr13:110436924-110440321	NB4	blood:	n/a	chr13:110438970-110438980 chr13:110439018-110439028 chr13:110439313-110439323
22	CTCF	chr13:110439692-110440247	K562	blood:	n/a	n/a
23	ZNF143	chr13:110439590-110440269	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr13:110438590-110440187	ProgFib	skin:	n/a	n/a
25	MAZ	chr13:110438706-110440328	K562	blood:	n/a	chr13:110439018-110439028 chr13:110439313-110439323
26	POLR2A	chr13:110433254-110440498	HL-60	blood:	n/a	n/a
27	POLR2A	chr13:110439836-110440119	K562	blood:	n/a	n/a
28	TBP	chr13:110438746-110440358	K562	blood:	n/a	n/a
29	POLR2A	chr13:110438529-110440199	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr13:110438656-110440437	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr13:110438707-110440292	K562	blood:	n/a	n/a
32	MAX	chr13:110438697-110440135	A549	lung:	n/a	chr13:110438970-110438980 chr13:110439018-110439028 chr13:110439313-110439323
33	POLR2A	chr13:110431310-110440354	Hela-S3	cervix:	n/a	n/a
34	MAX	chr13:110438749-110440354	NB4	blood:	n/a	chr13:110438970-110438980 chr13:110439018-110439028 chr13:110439313-110439323
35	CTCF	chr13:110439980-110440130	K562	blood:	n/a	n/a
36	POLR2A	chr13:110436680-110440263	MCF-7	breast:	n/a	n/a
37	POLR2A	chr13:110438718-110440105	K562	blood:	n/a	n/a
38	POLR2A	chr13:110439095-110440334	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr13:110439434-110440077	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr13:110438692-110440206	GM18951	blood:	n/a	n/a
41	SMARCC1	chr13:110439433-110440299	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr13:110437519-110440391	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZNF263	chr13:110439499-110440053	HEK293-T-REx	kidney:	n/a	n/a
44	CCNT2	chr13:110438073-110440307	K562	blood:	n/a	chr13:110440103-110440112 chr13:110439148-110439157 chr13:110439278-110439287
45	MYC	chr13:110438769-110440337	K562	blood:	n/a	chr13:110438970-110438980 chr13:110439018-110439028 chr13:110439313-110439323
46	MAX	chr13:110438751-110440246	K562	blood:	n/a	chr13:110438970-110438980 chr13:110439018-110439028 chr13:110439313-110439323
47	CTCF	chr13:110439927-110440055	GM19239	blood:	n/a	n/a
48	EP300	chr13:110438614-110440130	SK-N-SH	brain:	n/a	chr13:110438689-110438698 chr13:110439009-110439025 chr13:110439008-110439024
49	CTCF	chr13:110439960-110440110	HEK293	kidney:	n/a	n/a
50	POLR2A	chr13:110440042-110440218	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:110439408..110440218-chr17:26368504..26369181,2	Hela-S3	cervix:
2	chr13:110355569..110358710-chr13:110439541..110442319,3	MCF-7	breast:
3	chr13:110439300..110440162-chr3:50336111..50336962,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL4A2-3	chr13:110439457-110442761	NONHSAT035120

Variant related genes	Relation type
IRS2	TF binding region
ENSG00000186792	Chromatin interaction
ENSG00000087095	Chromatin interaction
ENSG00000243477	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826788	chr13:110381750-110469062	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv826789	chr13:110387268-110473524	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv826790	chr13:110395165-110463032	Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv826791	chr13:110397733-110462553	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv826792	chr13:110398678-110462209	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1047427	chr13:110412864-110446417	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv826793	chr13:110423187-110448628	Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv826794	chr13:110424916-110448628	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
9	nsv826795	chr13:110425465-110448628	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
10	nsv826796	chr13:110430886-110442431	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	n/a
11	esv1834749	chr13:110431891-110441483	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	n/a
12	esv3502965	chr13:110433651-110441049	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	n/a
13	esv18455	chr13:110433668-110440305	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	n/a
14	nsv563088	chr13:110434310-110440278	Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	n/a
15	esv1792707	chr13:110435953-110440278	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
16	esv1836001	chr13:110435953-110440278	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
17	esv1795605	chr13:110435953-110441483	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
18	esv1841056	chr13:110435953-110441483	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
19	esv1795443	chr13:110435953-110453607	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
20	esv3362839	chr13:110436851-110440249	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	n/a
21	esv3375101	chr13:110437776-110440824	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
22	esv3387456	chr13:110437801-110440099	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110434000-110440200	Active TSS	Hela-S3	cervix
2	chr13:110434400-110440200	Active TSS	HSMM	muscle
3	chr13:110435000-110440400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:110435800-110440400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr13:110436000-110440400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr13:110436000-110440600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr13:110436000-110441000	Active TSS	HSMMtube	muscle
8	chr13:110436200-110440400	Active TSS	Brain Angular Gyrus	brain
9	chr13:110436200-110440400	Active TSS	Colon Smooth Muscle	Colon
10	chr13:110436200-110441000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr13:110436400-110440400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:110436400-110440400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr13:110436400-110440400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:110436400-110440600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr13:110436400-110440600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr13:110436600-110440200	Active TSS	Duodenum Mucosa	Duodenum
17	chr13:110436600-110440200	Active TSS	NHEK	skin
18	chr13:110436600-110440400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:110436600-110440400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:110436600-110440400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr13:110436600-110440400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr13:110436600-110440400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr13:110436600-110440800	Weak transcription	Fetal Heart	heart
24	chr13:110436800-110440200	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr13:110436800-110440200	Active TSS	Small Intestine	intestine
26	chr13:110436800-110440200	Active TSS	NH-A	brain
27	chr13:110436800-110440400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr13:110436800-110440400	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr13:110436800-110440400	Active TSS	NHDF-Ad	bronchial
30	chr13:110436800-110440600	Active TSS	HMEC	breast
31	chr13:110437000-110440400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:110437000-110440400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:110437000-110440400	Active TSS	Aorta	Aorta
34	chr13:110437000-110440400	Active TSS	Brain Cingulate Gyrus	brain
35	chr13:110437000-110440400	Active TSS	Ovary	ovary
36	chr13:110437000-110440400	Active TSS	Psoas Muscle	Psoas
37	chr13:110437000-110440400	Active TSS	Right Atrium	heart
38	chr13:110437000-110440400	Active TSS	NHLF	lung
39	chr13:110437400-110440200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:110437400-110440200	Active TSS	Fetal Kidney	kidney
41	chr13:110437400-110440200	Active TSS	Fetal Lung	lung
42	chr13:110437800-110440200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr13:110437800-110440200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr13:110437800-110440200	Active TSS	Gastric	stomach
45	chr13:110437800-110440200	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr13:110437800-110440200	Active TSS	Stomach Smooth Muscle	stomach
47	chr13:110437800-110440400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr13:110437800-110440400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:110437800-110440400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:110437800-110441000	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links