Variant report

Variant	rs562679490
Chromosome Location	chr18:12658869-12658870
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	REST	chr18:12656487-12659001	H1-neurons	neurons:	n/a	chr18:12657226-12657239 chr18:12657214-12657227 chr18:12657237-12657257 chr18:12657223-12657232 chr18:12657237-12657257 chr18:12657238-12657256 chr18:12657344-12657357
2	NR2F2	chr18:12658059-12658894	MCF-7	breast:	n/a	n/a
3	SIN3A	chr18:12657617-12658947	H1-hESC	embryonic stem cell:	n/a	chr18:12657869-12657880 chr18:12657876-12657889
4	HA-E2F1	chr18:12658453-12658905	MCF-7	breast:	n/a	chr18:12658504-12658518
5	CTCF	chr18:12658720-12658870	HVMF	connective:	n/a	n/a
6	CTCF	chr18:12658840-12658990	NHDF-neo	bronchial:	n/a	n/a
7	CTCF	chr18:12658720-12658870	MCF-7	breast:	n/a	n/a
8	TFAP2C	chr18:12657624-12658900	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr18:12658547-12658905	H1-hESC	embryonic stem cell:	n/a	chr18:12658757-12658769
10	ZNF263	chr18:12657645-12659434	HEK293-T-REx	kidney:	n/a	chr18:12659328-12659349 chr18:12659330-12659339
11	CTCF	chr18:12658800-12658950	BJ	skin:	n/a	n/a
12	USF2	chr18:12658738-12658923	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAZ	chr18:12656513-12658995	IMR90	lung:	n/a	chr18:12658406-12658415
14	ARID3A	chr18:12658846-12659073	HepG2	liver:	n/a	n/a
15	CTCF	chr18:12658760-12658910	A549	lung:	n/a	n/a
16	CTCF	chr18:12658740-12658890	HPF	lung:	n/a	n/a
17	RAD21	chr18:12658583-12658950	SK-N-SH_RA	brain:	n/a	chr18:12658757-12658769
18	RAD21	chr18:12658041-12658951	H1-hESC	embryonic stem cell:	n/a	chr18:12658757-12658769
19	CHD1	chr18:12656380-12659102	IMR90	lung:	n/a	n/a
20	CTCF	chr18:12658720-12658870	AG04449	skin:	n/a	n/a
21	MXI1	chr18:12656516-12659443	SK-N-SH	brain:	n/a	n/a
22	MXI1	chr18:12656589-12658993	IMR90	lung:	n/a	n/a
23	SMC3	chr18:12657892-12658964	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr18:12658534-12658928	Hela-S3	cervix:	n/a	chr18:12658757-12658769

No.	Distal block	Cell Line	Cell type
1	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
2	chr18:12656018..12659900-chr18:12701056..12705601,5	K562	blood:
3	chr18:12406559..12410304-chr18:12656888..12659730,4	MCF-7	breast:
4	chr18:12654302..12656873-chr18:12657659..12659911,2	MCF-7	breast:
5	chr18:12418998..12421842-chr18:12658407..12660489,3	MCF-7	breast:
6	chr18:12418519..12420831-chr18:12657213..12660140,3	MCF-7	breast:
7	chr18:12657668..12659639-chr18:12701302..12703566,3	MCF-7	breast:
8	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
9	chr18:12435991..12438957-chr18:12658317..12660163,2	MCF-7	breast:
10	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
11	chr18:12404079..12409500-chr18:12655702..12659746,9	K562	blood:
12	chr18:12658848..12660471-chr18:12660520..12662160,2	MCF-7	breast:
13	chr18:12657085..12659648-chr18:12882376..12884207,2	K562	blood:

Variant related genes	Relation type
SPIRE1	TF binding region
ENSG00000134278	Chromatin interaction
ENSG00000267199	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000141391	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3397790	chr18:12649001-12673755	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	esv3436179	chr18:12655852-12660050	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	esv3323207	chr18:12656377-12658925	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv3424423	chr18:12656602-12659250	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv576507	chr18:12657195-12673187	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12653800-12670400	Weak transcription	Dnd41	blood
2	chr18:12655400-12659000	Active TSS	Brain Angular Gyrus	brain
3	chr18:12655400-12659000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr18:12655400-12659600	Active TSS	Fetal Brain Female	brain
5	chr18:12655800-12659000	Active TSS	NHLF	lung
6	chr18:12656000-12659000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:12656000-12659000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr18:12656000-12659000	Active TSS	HSMM	muscle
9	chr18:12656000-12659200	Active TSS	HSMMtube	muscle
10	chr18:12656200-12659400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr18:12656400-12659000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:12656400-12659000	Active TSS	Stomach Smooth Muscle	stomach
13	chr18:12656400-12659000	Active TSS	A549	lung
14	chr18:12656600-12659000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr18:12656600-12659000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr18:12656600-12659000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr18:12656600-12659000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr18:12656600-12659000	Active TSS	Fetal Muscle Trunk	muscle
19	chr18:12656600-12659000	Active TSS	Fetal Muscle Leg	muscle
20	chr18:12656600-12659000	Active TSS	Right Ventricle	heart
21	chr18:12656600-12659200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr18:12656800-12659000	Active TSS	Brain Substantia Nigra	brain
23	chr18:12656800-12659000	Active TSS	Fetal Stomach	stomach
24	chr18:12656800-12659000	Active TSS	Left Ventricle	heart
25	chr18:12656800-12659000	Active TSS	Ovary	ovary
26	chr18:12656800-12659200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr18:12657000-12659000	Active TSS	Brain Hippocampus Middle	brain
28	chr18:12657000-12659000	Active TSS	Colon Smooth Muscle	Colon
29	chr18:12657000-12659000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr18:12657000-12659200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr18:12657000-12659200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr18:12657200-12659000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr18:12657200-12659000	Active TSS	Fetal Intestine Small	intestine
34	chr18:12657200-12659000	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr18:12657400-12659000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr18:12657400-12659000	Active TSS	Colonic Mucosa	Colon
37	chr18:12657400-12659400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr18:12658000-12672800	Weak transcription	K562	blood
39	chr18:12658200-12659000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr18:12658200-12659000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr18:12658200-12659000	Flanking Active TSS	Liver	Liver
42	chr18:12658400-12659000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr18:12658400-12659000	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr18:12658400-12659000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr18:12658400-12659000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:12658400-12659000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr18:12658400-12659000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
48	chr18:12658400-12674000	Weak transcription	Spleen	Spleen
49	chr18:12658600-12659000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr18:12658600-12659000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links