Variant report

Variant	rs4237861
Chromosome Location	chr12:72667687-72667688
allele	A/C
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	CHD1	chr12:72664483-72669298	IMR90	lung:	n/a	chr12:72665403-72665413 chr12:72666399-72666409
2	POLR2A	chr12:72667419-72667955	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr12:72665033-72667943	H1-neurons	neurons:	n/a	n/a
4	MAZ	chr12:72665018-72668139	IMR90	lung:	n/a	chr12:72666392-72666402 chr12:72667571-72667581
5	SUZ12	chr12:72666596-72667919	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr12:72666477-72667733	H1-hESC	embryonic stem cell:	n/a	chr12:72667571-72667581
7	MXI1	chr12:72664946-72668220	IMR90	lung:	n/a	n/a
8	CTBP2	chr12:72665112-72668036	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr12:72665140-72667917	H1-hESC	embryonic stem cell:	n/a	n/a

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

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

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10506650	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10506652	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10784960	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879387	0.90[EUR][1000 genomes]
rs10879391	0.97[EUR][1000 genomes]
rs10879392	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10879394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879398	0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs11179146	0.95[EUR][1000 genomes]
rs11609294	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12229324	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17110954	0.85[JPT][hapmap]
rs3803030	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs4073007	0.85[JPT][hapmap]
rs4254109	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs4262761	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs4360737	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4423229	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4584622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587772	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4639975	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760827	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760829	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs6421234	0.83[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs7135786	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs7295741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307765	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7963246	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974998	0.94[EUR][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:91 , 50 per page) page: 1 2

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	chr12:72663200-72670200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:72663200-72671200	Active TSS	NH-A	brain
4	chr12:72663400-72667800	Active TSS	Ovary	ovary
5	chr12:72663400-72669400	Active TSS	Right Atrium	heart
6	chr12:72664800-72667800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:72664800-72667800	Active TSS	HMEC	breast
8	chr12:72664800-72668000	Bivalent/Poised TSS	NHLF	lung
9	chr12:72665000-72667800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:72665000-72667800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:72665000-72667800	Active TSS	Aorta	Aorta
12	chr12:72665000-72668000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr12:72665000-72668000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:72665000-72668200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:72665000-72668200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:72665000-72668600	Bivalent/Poised TSS	Osteobl	bone
17	chr12:72665200-72667800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:72665200-72667800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
19	chr12:72665200-72668000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr12:72665200-72668000	Bivalent/Poised TSS	HSMM	muscle
21	chr12:72665200-72668200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:72665400-72667800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:72665400-72668000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr12:72665600-72667800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr12:72665800-72668800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
26	chr12:72665800-72671400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:72666000-72667800	Bivalent Enhancer	Placenta	Placenta
28	chr12:72666000-72668000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr12:72666000-72668200	Bivalent Enhancer	Fetal Brain Male	brain
30	chr12:72666000-72668200	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr12:72666200-72667800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:72666200-72668200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
33	chr12:72666400-72667800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr12:72666400-72668000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr12:72666400-72668200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:72666600-72667800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:72666600-72667800	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
38	chr12:72666600-72667800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr12:72666600-72668000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:72666600-72668000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
41	chr12:72666600-72668000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
42	chr12:72666600-72668000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
43	chr12:72666600-72668200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
44	chr12:72666800-72667800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:72666800-72668000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr12:72666800-72668000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:72666800-72668000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:72666800-72668000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr12:72667000-72667800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr12:72667000-72667800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum

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