Variant report

Variant	rs376503918
Chromosome Location	chr3:42543425-42543426
allele	A/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	CTCF	chr3:42543092-42543498	K562	blood:	n/a	n/a
2	CTCF	chr3:42543195-42543468	Fibrobl	skin:	n/a	n/a
3	RAD21	chr3:42543164-42543516	HepG2	liver:	n/a	chr3:42543474-42543483
4	CTCF	chr3:42543239-42543430	Medullo	brain:	n/a	n/a
5	ZMIZ1	chr3:42543270-42543473	K562	blood:	n/a	n/a
6	CTCF	chr3:42543199-42543437	Kidney_OC	kidney:	n/a	n/a
7	CTCF	chr3:42543187-42543502	IMR90	lung:	n/a	n/a
8	CTCF	chr3:42543139-42543534	T-47D	breast:	n/a	n/a
9	SMC3	chr3:42543156-42543521	K562	blood:	n/a	n/a
10	RAD21	chr3:42543212-42543471	SK-N-SH_RA	brain:	n/a	n/a
11	RAD21	chr3:42543197-42543509	IMR90	lung:	n/a	chr3:42543474-42543483
12	CTCF	chr3:42543212-42543464	HUVEC	blood vessel:	n/a	n/a
13	EBF1	chr3:42543172-42543484	GM12878	blood:	n/a	chr3:42543360-42543371 chr3:42543361-42543370 chr3:42543361-42543371 chr3:42543361-42543370
14	RAD21	chr3:42543128-42543597	HepG2	liver:	n/a	chr3:42543474-42543483
15	TCF7L2	chr3:42543321-42544249	HCT-116	colon:	n/a	n/a
16	BACH1	chr3:42543207-42544084	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr3:42543157-42543467	K562	blood:	n/a	n/a
18	CTCF	chr3:42543140-42543528	K562	blood:	n/a	n/a
19	RAD21	chr3:42543126-42543520	SK-N-SH_RA	brain:	n/a	chr3:42543474-42543483
20	YY1	chr3:42543107-42543523	K562	blood:	n/a	n/a
21	CTCF	chr3:42543280-42543430	HEEpiC	esophagus:	n/a	n/a
22	CTCF	chr3:42543241-42543451	GM10266	blood:	n/a	n/a
23	MAX	chr3:42543267-42543444	K562	blood:	n/a	n/a
24	BHLHE40	chr3:42543250-42543741	K562	blood:	n/a	chr3:42543286-42543302
25	CTCF	chr3:42543280-42543430	GM12874	blood:	n/a	n/a
26	CTCF	chr3:42543164-42543482	T-47D	breast:	n/a	n/a
27	CTCF	chr3:42543067-42543662	K562	blood:	n/a	n/a
28	RAD21	chr3:42543133-42543526	HepG2	liver:	n/a	chr3:42543474-42543483
29	CTCF	chr3:42543215-42543466	ProgFib	skin:	n/a	n/a
30	CTCF	chr3:42543211-42543480	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr3:42543173-42543496	NHEK	skin:	n/a	n/a
32	CTCF	chr3:42543280-42543430	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr3:42543153-42543487	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZNF143	chr3:42543206-42543470	GM12878	blood:	n/a	n/a
35	CTCF	chr3:42543202-42543468	GM13977	blood:	n/a	n/a
36	CTCF	chr3:42543280-42543430	AoAF	blood vessel:	n/a	n/a
37	GTF2F1	chr3:42543388-42543470	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:42543400-42543550	WI-38	lung:	n/a	n/a
39	CTCF	chr3:42543320-42543470	HFF-Myc	foreskin:	n/a	n/a
40	CTCF	chr3:42543222-42543432	HepG2	liver:	n/a	n/a
41	TEAD4	chr3:42543042-42543426	K562	blood:	n/a	n/a
42	SMC3	chr3:42543224-42543493	GM12878	blood:	n/a	n/a
43	CTCF	chr3:42543280-42543430	RPTEC	kidney:	n/a	n/a
44	CTCF	chr3:42543280-42543430	HAc	cerebellar:	n/a	n/a
45	RAD21	chr3:42543234-42543446	K562	blood:	n/a	n/a
46	CTCF	chr3:42543216-42543434	GM13976	blood:	n/a	n/a
47	CTCF	chr3:42543094-42543537	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr3:42543208-42543458	SK-N-SH_RA	brain:	n/a	n/a
49	RAD21	chr3:42543058-42543495	H1-hESC	embryonic stem cell:	n/a	chr3:42543474-42543483 chr3:42543069-42543079
50	CTCF	chr3:42543300-42543450	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
2	chr3:42542597..42545270-chr3:42568668..42571142,2	K562	blood:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3435194	chr3:42543398-42545496	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42542000-42544800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:42542200-42545200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:42542400-42544600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:42542600-42543600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
5	chr3:42542600-42544000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
7	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
8	chr3:42542600-42544400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:42542600-42544800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:42542600-42545000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:42542600-42545200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:42542600-42545200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:42542800-42543600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
14	chr3:42542800-42543600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
15	chr3:42542800-42543600	Bivalent/Poised TSS	HSMMtube	muscle
16	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:42542800-42543800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
20	chr3:42542800-42544000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
22	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
23	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
24	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
25	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
26	chr3:42542800-42544600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:42542800-42544800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:42543000-42543600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
29	chr3:42543000-42543800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:42543000-42543800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:42543000-42543800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr3:42543000-42543800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:42543000-42543800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr3:42543000-42543800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:42543000-42543800	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr3:42543000-42543800	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr3:42543000-42543800	Bivalent Enhancer	Fetal Brain Male	brain
38	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	Placenta	Placenta
39	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
40	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
41	chr3:42543000-42543800	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr3:42543000-42544000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
44	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:42543000-42544000	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
48	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
49	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr3:42543000-42544000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links