Variant report

Variant	rs55730005
Chromosome Location	chr12:121157536-121157537
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr12:121157096-121157617	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:121157422-121157590	GM12878	blood:	n/a	n/a
3	FOXA1	chr12:121156936-121157589	HepG2	liver:	n/a	n/a
4	GATA1	chr12:121156872-121159133	PBDE	blood:	n/a	chr12:121156987-121157004 chr12:121157071-121157088
5	FOXA1	chr12:121156996-121157594	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121093291..121095008-chr12:121156747..121158862,2	K562	blood:
2	chr12:121092173..121095008-chr12:121157362..121160379,3	K562	blood:
3	chr12:120984201..120985776-chr12:121156791..121158435,2	MCF-7	breast:
4	chr12:121156734..121158293-chr12:121340769..121342837,2	MCF-7	breast:
5	chr12:121123639..121125451-chr12:121157117..121158712,2	MCF-7	breast:
6	chr12:121155674..121159047-chr12:121162083..121163846,4	MCF-7	breast:
7	chr12:121017670..121019248-chr12:121156331..121159030,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4700	TF binding region
ENSG00000122971	Chromatin interaction
ENSG00000022840	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000157837	Chromatin interaction
ENSG00000157782	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10431385	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12311479	0.84[ASN][1000 genomes]
rs12828810	0.97[ASN][1000 genomes]
rs12829722	0.97[ASN][1000 genomes]
rs2005455	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2066938	0.97[ASN][1000 genomes]
rs2239758	0.90[ASN][1000 genomes]
rs2239760	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2948149	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3021337	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3021338	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34030695	0.97[ASN][1000 genomes]
rs34734847	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35360964	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35525135	0.90[ASN][1000 genomes]
rs35599677	0.90[ASN][1000 genomes]
rs35771722	0.97[ASN][1000 genomes]
rs3752531	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3999408	0.90[ASN][1000 genomes]
rs548093	0.87[EUR][1000 genomes]
rs556001	0.87[EUR][1000 genomes]
rs56273049	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57830821	0.85[ASN][1000 genomes]
rs60858026	0.90[ASN][1000 genomes]
rs6490300	0.80[EUR][1000 genomes]
rs695948	0.87[EUR][1000 genomes]
rs695949	0.84[EUR][1000 genomes]
rs696337	0.80[EUR][1000 genomes]
rs71454661	0.90[ASN][1000 genomes]
rs7306541	0.90[ASN][1000 genomes]
rs7313271	0.97[ASN][1000 genomes]
rs998727	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121149600-121159000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:121149800-121157600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:121149800-121162800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:121150000-121163000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:121150400-121157800	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:121150400-121161600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:121150400-121163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:121150600-121158400	Strong transcription	NH-A	brain
9	chr12:121150800-121162400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:121150800-121162400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:121151000-121158200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:121151000-121158200	Strong transcription	HMEC	breast
13	chr12:121151000-121161200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr12:121151000-121161800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:121151000-121161800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:121151000-121162200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:121151000-121163000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:121151200-121157800	Strong transcription	NHLF	lung
19	chr12:121151200-121158000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:121151200-121158000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:121151200-121158000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:121151200-121158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:121151200-121158200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr12:121151200-121158200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:121151200-121158600	Strong transcription	NHEK	skin
26	chr12:121151200-121160400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:121151200-121160600	Strong transcription	Lung	lung
28	chr12:121151200-121161200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr12:121151200-121161200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:121151200-121161200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:121151200-121161200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr12:121151200-121161200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr12:121151200-121161200	Strong transcription	Hela-S3	cervix
34	chr12:121151200-121161200	Strong transcription	HUVEC	blood vessel
35	chr12:121151200-121161400	Strong transcription	Fetal Muscle Leg	muscle
36	chr12:121151200-121161600	Strong transcription	Ovary	ovary
37	chr12:121151200-121161800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:121151200-121162000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:121151200-121162200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:121151200-121162200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:121151200-121162200	Strong transcription	Brain Anterior Caudate	brain
42	chr12:121151200-121162200	Strong transcription	Fetal Thymus	thymus
43	chr12:121151200-121162400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:121151200-121162600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:121151200-121162600	Strong transcription	Fetal Stomach	stomach
46	chr12:121151200-121163000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:121151400-121163600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:121151600-121159000	Weak transcription	Right Atrium	heart
49	chr12:121151800-121157800	Strong transcription	Brain Cingulate Gyrus	brain
50	chr12:121151800-121158000	Strong transcription	A549	lung

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