Variant report

Variant	rs182921
Chromosome Location	chr3:42543274-42543275
allele	A/T
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	chr3:42543240-42543390	AoAF	blood vessel:	n/a	n/a
2	CTCF	chr3:42543092-42543498	K562	blood:	n/a	n/a
3	CTCF	chr3:42543260-42543410	GM12872	blood:	n/a	n/a
4	CTCF	chr3:42543195-42543468	Fibrobl	skin:	n/a	n/a
5	RAD21	chr3:42543164-42543516	HepG2	liver:	n/a	chr3:42543474-42543483
6	CTCF	chr3:42543240-42543390	GM12867	blood:	n/a	n/a
7	CTCF	chr3:42543260-42543410	HFF-Myc	foreskin:	n/a	n/a
8	CTCF	chr3:42543260-42543410	HPF	lung:	n/a	n/a
9	CTCF	chr3:42543239-42543430	Medullo	brain:	n/a	n/a
10	ZMIZ1	chr3:42543270-42543473	K562	blood:	n/a	n/a
11	ARID3A	chr3:42543260-42543326	HepG2	liver:	n/a	n/a
12	CTCF	chr3:42543199-42543437	Kidney_OC	kidney:	n/a	n/a
13	CTCF	chr3:42543187-42543502	IMR90	lung:	n/a	n/a
14	CTCF	chr3:42543139-42543534	T-47D	breast:	n/a	n/a
15	SMC3	chr3:42543156-42543521	K562	blood:	n/a	n/a
16	CTCF	chr3:42543260-42543410	BJ	skin:	n/a	n/a
17	CTCF	chr3:42543240-42543390	HepG2	liver:	n/a	n/a
18	RAD21	chr3:42543212-42543471	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr3:42543197-42543509	IMR90	lung:	n/a	chr3:42543474-42543483
20	CTCF	chr3:42543212-42543464	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr3:42543204-42543400	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr3:42543240-42543390	GM12866	blood:	n/a	n/a
23	EBF1	chr3:42543172-42543484	GM12878	blood:	n/a	chr3:42543360-42543371 chr3:42543361-42543370 chr3:42543361-42543371 chr3:42543361-42543370
24	CTCF	chr3:42543260-42543410	AG09309	skin:	n/a	n/a
25	RAD21	chr3:42543128-42543597	HepG2	liver:	n/a	chr3:42543474-42543483
26	CTCF	chr3:42543260-42543410	NHEK	skin:	n/a	n/a
27	CTCF	chr3:42543220-42543370	HEEpiC	esophagus:	n/a	n/a
28	CTCF	chr3:42543240-42543390	GM12868	blood:	n/a	n/a
29	CTCF	chr3:42543220-42543370	GM12870	blood:	n/a	n/a
30	BACH1	chr3:42543207-42544084	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr3:42543157-42543467	K562	blood:	n/a	n/a
32	CTCF	chr3:42543140-42543528	K562	blood:	n/a	n/a
33	RAD21	chr3:42543126-42543520	SK-N-SH_RA	brain:	n/a	chr3:42543474-42543483
34	YY1	chr3:42543107-42543523	K562	blood:	n/a	n/a
35	CTCF	chr3:42543260-42543410	GM12875	blood:	n/a	n/a
36	CTCF	chr3:42543220-42543370	GM12871	blood:	n/a	n/a
37	CTCF	chr3:42543241-42543451	GM10266	blood:	n/a	n/a
38	CTCF	chr3:42543260-42543410	HRE	kidney:	n/a	n/a
39	MAX	chr3:42543267-42543444	K562	blood:	n/a	n/a
40	BHLHE40	chr3:42543250-42543741	K562	blood:	n/a	chr3:42543286-42543302
41	CTCF	chr3:42543240-42543390	AG09309	skin:	n/a	n/a
42	CTCF	chr3:42543164-42543482	T-47D	breast:	n/a	n/a
43	CTCF	chr3:42543067-42543662	K562	blood:	n/a	n/a
44	RAD21	chr3:42543133-42543526	HepG2	liver:	n/a	chr3:42543474-42543483
45	CTCF	chr3:42543215-42543466	ProgFib	skin:	n/a	n/a
46	CTCF	chr3:42543220-42543370	HCM	heart:	n/a	n/a
47	CTCF	chr3:42543211-42543480	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr3:42543173-42543496	NHEK	skin:	n/a	n/a
49	CTCF	chr3:42543220-42543370	HBMEC	blood vessel:	n/a	n/a
50	CTCF	chr3:42543240-42543390	GM12865	blood:	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: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1078008	0.91[EUR][1000 genomes]
rs342542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399582	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406683	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs421558	0.81[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248806	0.82[AMR][1000 genomes]
rs673560	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:114 , 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	chr3:42542400-42543400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr3:42542400-42543400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr3:42542400-42544600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:42542600-42543600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
7	chr3:42542600-42544000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr3:42542600-42544200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
10	chr3:42542600-42544400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:42542600-42544800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr3:42542600-42545000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:42542600-42545200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:42542600-42545200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:42542800-42543400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:42542800-42543400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
17	chr3:42542800-42543400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
18	chr3:42542800-42543400	Transcr. at gene 5' and 3'	Right Atrium	heart
19	chr3:42542800-42543400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
20	chr3:42542800-42543600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
21	chr3:42542800-42543600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
22	chr3:42542800-42543600	Bivalent/Poised TSS	HSMMtube	muscle
23	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:42542800-42543800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:42542800-42543800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
27	chr3:42542800-42544000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr3:42542800-42544000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
31	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr3:42542800-42544200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
33	chr3:42542800-42544600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr3:42542800-42544800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:42543000-42543400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:42543000-42543400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
37	chr3:42543000-42543400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
38	chr3:42543000-42543400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
39	chr3:42543000-42543400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
40	chr3:42543000-42543400	Enhancers	Liver	Liver
41	chr3:42543000-42543400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:42543000-42543400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
43	chr3:42543000-42543400	Bivalent Enhancer	Psoas Muscle	Psoas
44	chr3:42543000-42543400	Flanking Active TSS	Right Ventricle	heart
45	chr3:42543000-42543600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
46	chr3:42543000-42543800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:42543000-42543800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:42543000-42543800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr3:42543000-42543800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:42543000-42543800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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