Variant report

Variant	rs2720030
Chromosome Location	chr12:122181123-122181124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr12:122180614-122181306	K562	blood:	n/a	n/a
2	HCFC1	chr12:122180874-122181195	K562	blood:	n/a	n/a
3	ATF1	chr12:122180824-122181237	K562	blood:	n/a	n/a
4	JUND	chr12:122180705-122181374	K562	blood:	n/a	n/a
5	BHLHE40	chr12:122180827-122181335	K562	blood:	n/a	n/a
6	KAP1	chr12:122180782-122181135	U2OS	brain:	n/a	n/a
7	MYC	chr12:122181085-122181159	K562	blood:	n/a	n/a
8	POLR2A	chr12:122180901-122181267	HUVEC	blood vessel:	n/a	n/a
9	MAZ	chr12:122180780-122181246	K562	blood:	n/a	n/a
10	FOSL2	chr12:122180943-122181323	A549	lung:	n/a	n/a
11	FOS	chr12:122180950-122181330	HUVEC	blood vessel:	n/a	chr12:122181184-122181195
12	RCOR1	chr12:122180706-122181357	K562	blood:	n/a	n/a
13	EP300	chr12:122180704-122181297	K562	blood:	n/a	n/a
14	JUN	chr12:122180694-122181897	K562	blood:	n/a	n/a
15	TEAD4	chr12:122180691-122181231	K562	blood:	n/a	n/a
16	GTF3C2	chr12:122180531-122181430	K562	blood:	n/a	n/a
17	FOSL1	chr12:122181047-122181248	K562	blood:	n/a	chr12:122181184-122181195
18	ARID3A	chr12:122180751-122181242	K562	blood:	n/a	n/a
19	CUX1	chr12:122180972-122181178	K562	blood:	n/a	n/a
20	ATF3	chr12:122180935-122181287	K562	blood:	n/a	n/a
21	TBL1XR1	chr12:122180765-122181255	K562	blood:	n/a	n/a
22	JUN	chr12:122180959-122181287	K562	blood:	n/a	n/a
23	FOSL1	chr12:122180969-122181301	K562	blood:	n/a	chr12:122181184-122181195
24	RCOR1	chr12:122181002-122181253	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122180813..122182540-chr12:122189739..122192360,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM120B	TF binding region
ENSG00000188735	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10840614	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10840615	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12814021	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2669170	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2720031	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651018	0.81[EUR][1000 genomes]
rs2942373	0.84[EUR][1000 genomes]
rs2954114	0.87[EUR][1000 genomes]
rs34933970	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv560459	chr12:122167095-122185780	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
5	nsv560460	chr12:122177322-122185780	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv560461	chr12:122177322-122185846	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv560462	chr12:122177322-122186071	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122151600-122186200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:122152000-122182200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:122152000-122188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:122152200-122181600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:122152200-122181800	Weak transcription	Right Ventricle	heart
6	chr12:122152200-122186400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:122152200-122188000	Weak transcription	Brain Germinal Matrix	brain
8	chr12:122152200-122188000	Weak transcription	Dnd41	blood
9	chr12:122152200-122191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:122152200-122191600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:122152200-122200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:122152400-122188000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:122152800-122186200	Weak transcription	Pancreas	Pancrea
14	chr12:122154000-122182200	Weak transcription	Primary T cells from cord blood	blood
15	chr12:122154200-122200400	Weak transcription	Psoas Muscle	Psoas
16	chr12:122155200-122181600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:122155200-122182400	Weak transcription	NHEK	skin
18	chr12:122155200-122186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:122155600-122186200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:122157200-122182400	Weak transcription	GM12878-XiMat	blood
21	chr12:122158800-122186200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:122158800-122186200	Weak transcription	NHDF-Ad	bronchial
23	chr12:122158800-122186400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:122159000-122186200	Weak transcription	NH-A	brain
25	chr12:122159200-122181600	Weak transcription	NHLF	lung
26	chr12:122159200-122186400	Weak transcription	HSMM	muscle
27	chr12:122159400-122194800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:122159600-122181600	Weak transcription	Brain Angular Gyrus	brain
29	chr12:122161800-122181600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:122163400-122181400	Weak transcription	Fetal Stomach	stomach
31	chr12:122163400-122186200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:122163600-122182000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:122163600-122186200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:122163600-122186200	Weak transcription	Liver	Liver
35	chr12:122163600-122186600	Weak transcription	HSMMtube	muscle
36	chr12:122163600-122188000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:122163600-122188200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:122163800-122182400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:122163800-122186200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:122164200-122181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:122164800-122188200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:122166800-122186200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:122166800-122186200	Weak transcription	Thymus	Thymus
44	chr12:122166800-122186400	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:122167200-122186400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:122167600-122186200	Weak transcription	Spleen	Spleen
47	chr12:122170400-122181600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:122170400-122181600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:122170400-122181600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:122170400-122186200	Weak transcription	Right Atrium	heart

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