Variant report

Variant	rs2232332
Chromosome Location	chr3:53880789-53880790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:98)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:98 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:53880054-53881071	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:53880304-53880865	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr3:53879623-53880964	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:53879609-53880847	H1-hESC	embryonic stem cell:	n/a	n/a
5	SETDB1	chr3:53880405-53880796	U2OS	brain:	n/a	n/a
6	MAX	chr3:53879779-53881032	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr3:53880114-53880814	HepG2	liver:	n/a	n/a
8	SIN3A	chr3:53879567-53880801	H1-hESC	embryonic stem cell:	n/a	chr3:53880057-53880068 chr3:53880681-53880694
9	POLR2A	chr3:53879742-53880851	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:53880160-53880993	HepG2	liver:	n/a	n/a
11	MAX	chr3:53879573-53880808	Hela-S3	cervix:	n/a	n/a
12	MAX	chr3:53880081-53880979	A549	lung:	n/a	n/a
13	MYBL2	chr3:53880155-53880937	HepG2	liver:	n/a	n/a
14	TCF12	chr3:53879870-53880918	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr3:53880218-53880796	HepG2	liver:	n/a	n/a
16	TBP	chr3:53879640-53880864	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:53880206-53880884	K562	blood:	n/a	n/a
18	MAX	chr3:53879200-53880964	HCT-116	colon:	n/a	n/a
19	MAX	chr3:53880177-53880873	H1-hESC	embryonic stem cell:	n/a	n/a
20	HEY1	chr3:53880130-53880924	HepG2	liver:	n/a	chr3:53880439-53880454
21	POLR2A	chr3:53879199-53880967	GM18526	blood:	n/a	n/a
22	MAX	chr3:53879218-53881061	HCT-116	colon:	n/a	n/a
23	POLR2A	chr3:53880209-53880838	GM15510	blood:	n/a	n/a
24	TBP	chr3:53880222-53880793	HepG2	liver:	n/a	n/a
25	E2F6	chr3:53880050-53880938	Hela-S3	cervix:	n/a	chr3:53880502-53880514
26	BHLHE40	chr3:53879719-53880817	GM12878	blood:	n/a	chr3:53880063-53880079
27	POLR2A	chr3:53876459-53880951	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:53880327-53880801	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:53879116-53881395	GM19099	blood:	n/a	n/a
30	POLR2A	chr3:53875240-53880984	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:53880235-53880824	HepG2	liver:	n/a	n/a
32	MAX	chr3:53880087-53880964	MCF-7	breast:	n/a	n/a
33	MAZ	chr3:53880237-53880912	HepG2	liver:	n/a	n/a
34	TAF1	chr3:53879538-53880864	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:53877904-53881035	GM19193	blood:	n/a	n/a
36	POLR2A	chr3:53877360-53880992	GM18951	blood:	n/a	n/a
37	ZNF263	chr3:53880116-53880955	HEK293-T-REx	kidney:	n/a	n/a
38	E2F6	chr3:53880058-53881204	H1-hESC	embryonic stem cell:	n/a	chr3:53880502-53880514
39	POLR2A	chr3:53880035-53880897	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:53879378-53881048	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr3:53879629-53880914	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:53880064-53880890	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:53880097-53880832	HCT-116	colon:	n/a	n/a
44	TCF7L2	chr3:53880054-53880844	HCT-116	colon:	n/a	n/a
45	MAX	chr3:53879461-53881088	A549	lung:	n/a	n/a
46	POLR2A	chr3:53880104-53880854	HepG2	liver:	n/a	n/a
47	TAF1	chr3:53880035-53880803	HepG2	liver:	n/a	n/a
48	MAX	chr3:53879403-53881107	HepG2	liver:	n/a	n/a
49	ARID3A	chr3:53880305-53880971	HepG2	liver:	n/a	n/a
50	E2F6	chr3:53880062-53881023	H1-hESC	embryonic stem cell:	n/a	chr3:53880502-53880514

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:53880775-53880825	SK-N-MC	brain:	n/a
2	chr3:53880775-53880825	HAEpiC	amniotic membrane:	n/a
3	chr3:53880775-53880825	HCPEpiC	choroid plexus:	n/a
4	chr3:53880775-53880825	SK-N-SH	brain:	n/a
5	chr3:53880775-53880825	NH-A	brain:	n/a
6	chr3:53880775-53880825	HCF	heart:	n/a
7	chr3:53880775-53880825	Hela-S3	cervix:	n/a
8	chr3:53880775-53880825	PANC-1	pancreas:	n/a
9	chr3:53880775-53880825	AG04450	lung:	fetal
10	chr3:53880775-53880825	PrEC	prostate:	n/a
11	chr3:53880775-53880825	ovcar-3	ovarian:	n/a
12	chr3:53880775-53880825	AG10803	skin:	n/a
13	chr3:53880775-53880825	MCF10A-Er-Src	breast:	n/a
14	chr3:53880775-53880825	T-47D	breast:	n/a
15	chr3:53880775-53880825	HRCEpiC	kidney:	n/a
16	chr3:53880775-53880825	MCF-7	breast:	n/a
17	chr3:53880775-53880825	NT2-D1	testis:	n/a
18	chr3:53880775-53880825	HEK293	kidney:	embryo
19	chr3:53880775-53880825	H1-hESC	embryonic stem cell:	embryo
20	chr3:53880775-53880825	PFSK-1	brain:	n/a
21	chr3:53880775-53880825	A549	lung:	n/a
22	chr3:53880775-53880825	RPTEC	kidney:	n/a
23	chr3:53880775-53880825	Caco-2	colon:	n/a
24	chr3:53880775-53880825	Hepatocyte	liver:	n/a
25	chr3:53880775-53880825	GM19239	blood:	n/a
26	chr3:53880775-53880825	IMR90	lung:	fetal
27	chr3:53880775-53880825	HNPCEpiC	eye:	n/a
28	chr3:53880775-53880825	AG09309	skin:	n/a
29	chr3:53880775-53880825	HL-60	blood:	n/a
30	chr3:53880775-53880825	HPAEpiC	pulmonary alveolar:	n/a
31	chr3:53880775-53880825	HUVEC	blood vessel:	n/a
32	chr3:53880775-53880825	BE2_C	brain:	n/a
33	chr3:53880775-53880825	HCM	heart:	n/a
34	chr3:53880775-53880825	U87	brain:	n/a
35	chr3:53880775-53880825	HepG2	liver:	n/a
36	chr3:53880775-53880825	HCT-116	colon:	n/a
37	chr3:53880775-53880825	SAEC	small airway:	n/a
38	chr3:53880775-53880825	GM12891	blood:	n/a
39	chr3:53880775-53880825	SKMC	muscle:	n/a
40	chr3:53880775-53880825	HIPEpiC	eye:	n/a
41	chr3:53880775-53880825	HEEpiC	esophagus:	n/a
42	chr3:53880775-53880825	LNCaP	prostate:	n/a
43	chr3:53880775-53880825	NB4	blood:	n/a
44	chr3:53880775-53880825	GM12878	blood:	n/a
45	chr3:53880775-53880825	NHDF-neo	bronchial:	n/a
46	chr3:53880775-53880825	BJ	skin:	n/a
47	chr3:53880775-53880825	GM12892	blood:	n/a
48	chr3:53880775-53880825	AG04449	skin:	fetal
49	chr3:53880775-53880825	HRE	kidney:	n/a
50	chr3:53880775-53880825	ProgFib	skin:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53526182..53528875-chr3:53879796..53881358,2	MCF-7	breast:
2	chr3:53288526..53291244-chr3:53879304..53881119,2	MCF-7	breast:
3	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

No data

Variant related genes	Relation type
CHDH	TF binding region
CHDH	CpG island
ENSG00000113812	Chromatin interaction
ENSG00000222888	Chromatin interaction
ENSG00000163931	Chromatin interaction
ENSG00000157388	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1025690	0.97[ASN][1000 genomes]
rs2884632	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4546140	0.88[ASN][1000 genomes]
rs7650883	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv876805	chr3:53865731-53883722	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53879200-53880800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:53879200-53881200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:53879200-53881200	Active TSS	Rectal Smooth Muscle	rectum
4	chr3:53879400-53880800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:53879400-53880800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:53879400-53880800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:53879400-53880800	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr3:53879400-53880800	Active TSS	Fetal Kidney	kidney
9	chr3:53879400-53880800	Bivalent/Poised TSS	HSMMtube	muscle
10	chr3:53879400-53881000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr3:53879400-53881000	Active TSS	A549	lung
12	chr3:53879400-53881200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:53879400-53881200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
14	chr3:53879400-53881400	Bivalent/Poised TSS	HepG2	liver
15	chr3:53879600-53880800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:53879600-53880800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr3:53879600-53880800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
18	chr3:53879600-53880800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
19	chr3:53879600-53880800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:53879600-53880800	Active TSS	Brain Angular Gyrus	brain
21	chr3:53879600-53880800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:53879600-53880800	Active TSS	Brain Substantia Nigra	brain
23	chr3:53879600-53880800	Active TSS	Hela-S3	cervix
24	chr3:53879600-53880800	Flanking Bivalent TSS/Enh	HMEC	breast
25	chr3:53879600-53881000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:53879600-53881000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:53879600-53881000	Active TSS	Brain Hippocampus Middle	brain
28	chr3:53879800-53880800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:53879800-53880800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr3:53879800-53880800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:53879800-53880800	Active TSS	Brain Cingulate Gyrus	brain
32	chr3:53879800-53880800	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr3:53879800-53880800	Active TSS	Stomach Mucosa	stomach
34	chr3:53879800-53880800	Bivalent/Poised TSS	Thymus	Thymus
35	chr3:53879800-53880800	Bivalent/Poised TSS	HUVEC	blood vessel
36	chr3:53879800-53880800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr3:53879800-53880800	Bivalent/Poised TSS	NHLF	lung
38	chr3:53879800-53881000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:53880000-53880800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr3:53880000-53881000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr3:53880000-53881000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
42	chr3:53880000-53881200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr3:53880000-53881200	Bivalent/Poised TSS	Fetal Brain Female	brain
44	chr3:53880200-53880800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:53880200-53880800	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:53880200-53880800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:53880200-53880800	Flanking Bivalent TSS/Enh	NHEK	skin
48	chr3:53880200-53881000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:53880200-53881400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:53880400-53880800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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