Variant report

Variant	rs2232330
Chromosome Location	chr3:53880367-53880368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:238)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:238 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:53879421-53880629	Hela-S3	cervix:	n/a	n/a
2	MAX	chr3:53880054-53881071	H1-hESC	embryonic stem cell:	n/a	n/a
3	NR2F2	chr3:53880146-53880690	MCF-7	breast:	n/a	n/a
4	SP1	chr3:53880230-53880783	HepG2	liver:	n/a	chr3:53880484-53880496
5	POLR2A	chr3:53880233-53880420	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:53880304-53880865	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr3:53880198-53880745	A549	lung:	n/a	n/a
8	CEBPB	chr3:53880283-53880471	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:53879623-53880964	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:53879609-53880847	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr3:53879779-53881032	H1-hESC	embryonic stem cell:	n/a	n/a
12	CHD2	chr3:53880266-53880507	GM12878	blood:	n/a	n/a
13	EP300	chr3:53880114-53880814	HepG2	liver:	n/a	n/a
14	SIN3A	chr3:53879567-53880801	H1-hESC	embryonic stem cell:	n/a	chr3:53880057-53880068 chr3:53880681-53880694
15	POLR2A	chr3:53879742-53880851	MCF-7	breast:	n/a	n/a
16	MYC	chr3:53880193-53880704	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:53880140-53880763	PANC-1	pancreas:	n/a	n/a
18	CCNT2	chr3:53880326-53880543	K562	blood:	n/a	n/a
19	ESR1	chr3:53880141-53880694	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr3:53880160-53880993	HepG2	liver:	n/a	n/a
21	MYC	chr3:53880207-53880568	MCF-7	breast:	n/a	n/a
22	MAX	chr3:53879573-53880808	Hela-S3	cervix:	n/a	n/a
23	MAX	chr3:53880081-53880979	A549	lung:	n/a	n/a
24	ESR1	chr3:53880260-53880540	ECC-1	luminal epithelium:	n/a	n/a
25	MYBL2	chr3:53880155-53880937	HepG2	liver:	n/a	n/a
26	ESR1	chr3:53880282-53880555	ECC-1	luminal epithelium:	n/a	n/a
27	MXI1	chr3:53879679-53880689	GM12878	blood:	n/a	n/a
28	CTCF	chr3:53880341-53880523	MCF-7	breast:	n/a	n/a
29	ZBTB7A	chr3:53880316-53880598	HepG2	liver:	n/a	n/a
30	ZEB1	chr3:53880162-53880586	GM12878	blood:	n/a	chr3:53880334-53880343 chr3:53880352-53880364
31	POLR2A	chr3:53880083-53880741	H1-hESC	embryonic stem cell:	n/a	n/a
32	TCF12	chr3:53879870-53880918	ECC-1	luminal epithelium:	n/a	n/a
33	CHD2	chr3:53880264-53880758	Hela-S3	cervix:	n/a	n/a
34	NFIC	chr3:53880218-53880796	HepG2	liver:	n/a	n/a
35	TBP	chr3:53879640-53880864	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:53880206-53880884	K562	blood:	n/a	n/a
37	SIN3AK20	chr3:53880171-53880477	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr3:53879200-53880964	HCT-116	colon:	n/a	n/a
39	MYBL2	chr3:53880183-53880688	HepG2	liver:	n/a	n/a
40	MAX	chr3:53880177-53880873	H1-hESC	embryonic stem cell:	n/a	n/a
41	HEY1	chr3:53880130-53880924	HepG2	liver:	n/a	chr3:53880439-53880454
42	CTCF	chr3:53880340-53880490	AG04449	skin:	n/a	n/a
43	CTCF	chr3:53880236-53880628	GM12878	blood:	n/a	n/a
44	TCF3	chr3:53880022-53880773	GM12878	blood:	n/a	n/a
45	CEBPB	chr3:53880290-53880553	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr3:53880280-53880430	GM12873	blood:	n/a	n/a
47	CTCF	chr3:53880280-53880430	GM12868	blood:	n/a	n/a
48	ESR1	chr3:53880262-53880607	T-47D	breast:	n/a	n/a
49	CTCF	chr3:53880300-53880450	GM12864	blood:	n/a	n/a
50	RCOR1	chr3:53880194-53880548	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:53880366-53880416	H1-hESC	embryonic stem cell:	embryo
2	chr3:53880366-53880416	GM12891	blood:	n/a
3	chr3:53880366-53880416	HCT-116	colon:	n/a
4	chr3:53880366-53880416	BJ	skin:	n/a
5	chr3:53880366-53880416	HPAEpiC	pulmonary alveolar:	n/a
6	chr3:53880366-53880416	AG04450	lung:	fetal
7	chr3:53880366-53880416	AG09309	skin:	n/a
8	chr3:53880366-53880416	PFSK-1	brain:	n/a
9	chr3:53880366-53880416	SK-N-MC	brain:	n/a
10	chr3:53880366-53880416	HepG2	liver:	n/a
11	chr3:53880366-53880416	SAEC	small airway:	n/a
12	chr3:53880366-53880416	U87	brain:	n/a
13	chr3:53880366-53880416	ovcar-3	ovarian:	n/a
14	chr3:53880366-53880416	BE2_C	brain:	n/a
15	chr3:53880366-53880416	HL-60	blood:	n/a
16	chr3:53880366-53880416	Hela-S3	cervix:	n/a
17	chr3:53880366-53880416	RPTEC	kidney:	n/a
18	chr3:53880366-53880416	HRE	kidney:	n/a
19	chr3:53880366-53880416	HAEpiC	amniotic membrane:	n/a
20	chr3:53880366-53880416	GM19239	blood:	n/a
21	chr3:53880366-53880416	HEEpiC	esophagus:	n/a
22	chr3:53880366-53880416	HRPEpiC	eye:	n/a
23	chr3:53880366-53880416	HRCEpiC	kidney:	n/a
24	chr3:53880366-53880416	HCM	heart:	n/a
25	chr3:53880366-53880416	LNCaP	prostate:	n/a
26	chr3:53880366-53880416	Hepatocyte	liver:	n/a
27	chr3:53880366-53880416	A549	lung:	n/a
28	chr3:53880366-53880416	HUVEC	blood vessel:	n/a
29	chr3:53880366-53880416	MCF10A-Er-Src	breast:	n/a
30	chr3:53880366-53880416	HMEC	breast:	n/a
31	chr3:53880366-53880416	SK-N-SH	brain:	n/a
32	chr3:53880366-53880416	GM12878	blood:	n/a
33	chr3:53880366-53880416	HEK293	kidney:	embryo
34	chr3:53880366-53880416	GM06990	blood:	n/a
35	chr3:53880366-53880416	SKMC	muscle:	n/a
36	chr3:53880366-53880416	HCPEpiC	choroid plexus:	n/a
37	chr3:53880366-53880416	NHDF-neo	bronchial:	n/a
38	chr3:53880366-53880416	NH-A	brain:	n/a
39	chr3:53880366-53880416	SK-N-SH_RA	brain:	n/a
40	chr3:53880366-53880416	NT2-D1	testis:	n/a
41	chr3:53880366-53880416	Caco-2	colon:	n/a
42	chr3:53880366-53880416	IMR90	lung:	fetal
43	chr3:53880366-53880416	PrEC	prostate:	n/a
44	chr3:53880366-53880416	AoSMC	blood vessel:	n/a
45	chr3:53880366-53880416	ECC-1	luminal epithelium:	n/a
46	chr3:53880366-53880416	NB4	blood:	n/a
47	chr3:53880366-53880416	T-47D	breast:	n/a
48	chr3:53880366-53880416	PANC-1	pancreas:	n/a
49	chr3:53880366-53880416	AG10803	skin:	n/a
50	chr3:53880366-53880416	Jurkat	blood:	n/a

(count:4 , 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	chr3:53879945..53880611-chr6:30028486..30029019,2	Hela-S3	cervix:
4	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

No data

Variant related genes	Relation type
CHDH	TF binding region
IL17RB	TF binding region
IL17RB	CpG island
CHDH	CpG island
ENSG00000157388	Chromatin interaction
ENSG00000222888	Chromatin interaction
ENSG00000163931	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2289205	0.91[ASN][1000 genomes]
rs3755817	0.91[ASN][1000 genomes]
rs62250937	0.82[ASN][1000 genomes]
rs62250939	0.82[ASN][1000 genomes]
rs920253	0.82[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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53879200-53880600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53879200-53880600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:53879200-53880800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:53879200-53881200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:53879200-53881200	Active TSS	Rectal Smooth Muscle	rectum
6	chr3:53879400-53880400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:53879400-53880600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:53879400-53880600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:53879400-53880600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:53879400-53880600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:53879400-53880600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:53879400-53880600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:53879400-53880600	Active TSS	Liver	Liver
14	chr3:53879400-53880600	Bivalent/Poised TSS	NHDF-Ad	bronchial
15	chr3:53879400-53880800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:53879400-53880800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:53879400-53880800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:53879400-53880800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:53879400-53880800	Active TSS	Fetal Kidney	kidney
20	chr3:53879400-53880800	Bivalent/Poised TSS	HSMMtube	muscle
21	chr3:53879400-53881000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
22	chr3:53879400-53881000	Active TSS	A549	lung
23	chr3:53879400-53881200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:53879400-53881200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr3:53879400-53881400	Bivalent/Poised TSS	HepG2	liver
26	chr3:53879600-53880400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:53879600-53880400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:53879600-53880400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:53879600-53880400	Active TSS	Small Intestine	intestine
30	chr3:53879600-53880400	Bivalent/Poised TSS	Osteobl	bone
31	chr3:53879600-53880600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:53879600-53880600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:53879600-53880600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:53879600-53880600	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr3:53879600-53880600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:53879600-53880600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:53879600-53880600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:53879600-53880600	Active TSS	Brain Anterior Caudate	brain
39	chr3:53879600-53880600	Active TSS	Colon Smooth Muscle	Colon
40	chr3:53879600-53880600	Active TSS	Duodenum Mucosa	Duodenum
41	chr3:53879600-53880600	Weak transcription	Fetal Heart	heart
42	chr3:53879600-53880600	Bivalent/Poised TSS	Fetal Stomach	stomach
43	chr3:53879600-53880600	Active TSS	Lung	lung
44	chr3:53879600-53880600	Active TSS	Ovary	ovary
45	chr3:53879600-53880600	Active TSS	Pancreas	Pancrea
46	chr3:53879600-53880600	Active TSS	Psoas Muscle	Psoas
47	chr3:53879600-53880600	Active TSS	Right Atrium	heart
48	chr3:53879600-53880600	Bivalent/Poised TSS	HSMM	muscle
49	chr3:53879600-53880600	Bivalent/Poised TSS	NH-A	brain
50	chr3:53879600-53880800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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