Variant report

Variant	rs4558203
Chromosome Location	chr12:72667550-72667551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr12:72664483-72669298	IMR90	lung:	n/a	chr12:72665403-72665413 chr12:72666399-72666409
2	POLR2A	chr12:72664488-72667607	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:72667419-72667955	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr12:72665033-72667943	H1-neurons	neurons:	n/a	n/a
5	MAZ	chr12:72665018-72668139	IMR90	lung:	n/a	chr12:72666392-72666402 chr12:72667571-72667581
6	SUZ12	chr12:72666596-72667919	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr12:72666477-72667733	H1-hESC	embryonic stem cell:	n/a	chr12:72667571-72667581
8	MXI1	chr12:72664946-72668220	IMR90	lung:	n/a	n/a
9	CTBP2	chr12:72665112-72668036	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr12:72665140-72667917	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:72667512-72667562	HAEpiC	amniotic membrane:	n/a
2	chr12:72667512-72667562	H1-hESC	embryonic stem cell:	embryo
3	chr12:72667526-72667576	NHBE	bronchial:	n/a
4	chr12:72667512-72667562	Hela-S3	cervix:	n/a
5	chr12:72667526-72667576	LNCaP	prostate:	n/a
6	chr12:72667526-72667576	GM19239	blood:	n/a
7	chr12:72667526-72667576	Jurkat	blood:	n/a
8	chr12:72667526-72667576	HNPCEpiC	eye:	n/a
9	chr12:72667512-72667562	GM12892	blood:	n/a
10	chr12:72667526-72667576	SK-N-MC	brain:	n/a
11	chr12:72667512-72667562	HCF	heart:	n/a
12	chr12:72667526-72667576	A549	lung:	n/a
13	chr12:72667512-72667562	AoSMC	blood vessel:	n/a
14	chr12:72667512-72667562	SAEC	small airway:	n/a
15	chr12:72667526-72667576	SKMC	muscle:	n/a
16	chr12:72667512-72667562	SK-N-SH	brain:	n/a
17	chr12:72667526-72667576	HPAEpiC	pulmonary alveolar:	n/a
18	chr12:72667512-72667562	SKMC	muscle:	n/a
19	chr12:72667512-72667562	HUVEC	blood vessel:	n/a
20	chr12:72667512-72667562	PrEC	prostate:	n/a
21	chr12:72667512-72667562	A549	lung:	n/a
22	chr12:72667512-72667562	HRPEpiC	eye:	n/a
23	chr12:72667512-72667562	CMK	blood:	n/a
24	chr12:72667526-72667576	AG09319	gingival:	n/a
25	chr12:72667512-72667562	NH-A	brain:	n/a
26	chr12:72667526-72667576	GM12878	blood:	n/a
27	chr12:72667526-72667576	ECC-1	luminal epithelium:	n/a
28	chr12:72667526-72667576	NT2-D1	testis:	n/a
29	chr12:72667526-72667576	AG04450	lung:	fetal
30	chr12:72667512-72667562	HCT-116	colon:	n/a
31	chr12:72667512-72667562	IMR90	lung:	fetal
32	chr12:72667512-72667562	BE2_C	brain:	n/a
33	chr12:72667512-72667562	HCPEpiC	choroid plexus:	n/a
34	chr12:72667526-72667576	BE2_C	brain:	n/a
35	chr12:72667512-72667562	AG10803	skin:	n/a
36	chr12:72667526-72667576	PrEC	prostate:	n/a
37	chr12:72667512-72667562	K562	blood:	n/a
38	chr12:72667512-72667562	HRCEpiC	kidney:	n/a
39	chr12:72667526-72667576	Caco-2	colon:	n/a
40	chr12:72667526-72667576	HRE	kidney:	n/a
41	chr12:72667512-72667562	MCF10A-Er-Src	breast:	n/a
42	chr12:72667512-72667562	PANC-1	pancreas:	n/a
43	chr12:72667512-72667562	BJ	skin:	n/a
44	chr12:72667526-72667576	HCM	heart:	n/a
45	chr12:72667526-72667576	MCF10A-Er-Src	breast:	n/a
46	chr12:72667512-72667562	HIPEpiC	eye:	n/a
47	chr12:72667526-72667576	HL-60	blood:	n/a
48	chr12:72667526-72667576	Hela-S3	cervix:	n/a
49	chr12:72667526-72667576	HIPEpiC	eye:	n/a
50	chr12:72667526-72667576	AG04449	skin:	fetal

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:72664308..72665953-chr12:72666174..72668987,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFC3H1-6	chr12:72667232-72667725	ENSG00000236333
2	lnc-ZFC3H1-6	chr12:72667550-72667580	NONHSAT029467

No data

Variant related genes	Relation type
TRHDE-AS1	TF binding region
TRHDE	TF binding region
TRHDE-AS1	CpG island
TRHDE	CpG island
ENSG00000236333	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10506649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879399	1.00[CEU][hapmap]
rs11179134	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829738	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300104	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306541	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311002	1.00[JPT][hapmap]
rs12318344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319940	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110963	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4312105	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350401	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4394875	0.85[ASN][1000 genomes]
rs7137961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969488	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7969786	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv559362	chr12:72641784-72694691	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72663000-72668400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:72663200-72667600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:72663200-72670200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:72663200-72671200	Active TSS	NH-A	brain
5	chr12:72663400-72667600	Active TSS	NHDF-Ad	bronchial
6	chr12:72663400-72667800	Active TSS	Ovary	ovary
7	chr12:72663400-72669400	Active TSS	Right Atrium	heart
8	chr12:72664800-72667800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:72664800-72667800	Active TSS	HMEC	breast
10	chr12:72664800-72668000	Bivalent/Poised TSS	NHLF	lung
11	chr12:72665000-72667800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:72665000-72667800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:72665000-72667800	Active TSS	Aorta	Aorta
14	chr12:72665000-72668000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:72665000-72668000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:72665000-72668200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:72665000-72668200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:72665000-72668600	Bivalent/Poised TSS	Osteobl	bone
19	chr12:72665200-72667600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr12:72665200-72667800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:72665200-72667800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr12:72665200-72668000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr12:72665200-72668000	Bivalent/Poised TSS	HSMM	muscle
24	chr12:72665200-72668200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:72665400-72667600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
26	chr12:72665400-72667600	Bivalent/Poised TSS	Thymus	Thymus
27	chr12:72665400-72667600	Bivalent/Poised TSS	A549	lung
28	chr12:72665400-72667800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:72665400-72668000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr12:72665600-72667800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr12:72665800-72667600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:72665800-72667600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:72665800-72667600	Active TSS	Fetal Intestine Small	intestine
34	chr12:72665800-72668800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:72665800-72671400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:72666000-72667800	Bivalent Enhancer	Placenta	Placenta
37	chr12:72666000-72668000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
38	chr12:72666000-72668200	Bivalent Enhancer	Fetal Brain Male	brain
39	chr12:72666000-72668200	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr12:72666200-72667800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:72666200-72668200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr12:72666400-72667600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
43	chr12:72666400-72667800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
44	chr12:72666400-72668000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
45	chr12:72666400-72668200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr12:72666600-72667600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:72666600-72667600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
48	chr12:72666600-72667600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:72666600-72667600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
50	chr12:72666600-72667600	Bivalent/Poised TSS	Brain Anterior Caudate	brain

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