Variant report

Variant	rs12058128
Chromosome Location	chr1:151106113-151106114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:151105411-151106236	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUN	chr1:151105969-151106119	H1-hESC	embryonic stem cell:	n/a	n/a
3	ELF1	chr1:151106104-151106597	GM12878	blood:	n/a	n/a
4	JUND	chr1:151105893-151106229	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF263	chr1:151106002-151106180	HEK293-T-REx	kidney:	n/a	chr1:151106006-151106015 chr1:151106143-151106164
6	MAX	chr1:151105069-151106289	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:151106069-151106204	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr1:151105540-151106276	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151103786..151106331-chr1:151117499..151120768,3	MCF-7	breast:
2	chr1:151106109..151108676-chr1:151117941..151119953,3	K562	blood:
3	chr1:151104790..151107252-chr1:151107376..151109485,2	K562	blood:
4	chr1:151104617..151106812-chr1:151117447..151119044,2	MCF-7	breast:
5	chr1:151106109..151110392-chr1:151117941..151122227,5	K562	blood:
6	chr1:151104720..151106721-chr1:151225505..151227550,2	MCF-7	breast:
7	chr1:151106097..151107684-chr1:151136573..151139445,2	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA6C	TF binding region
ENSG00000261168	TF binding region
ENSG00000159352	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11204774	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11204783	0.83[AFR][1000 genomes]
rs12060682	0.96[EUR][1000 genomes]
rs12070256	0.81[EUR][1000 genomes]
rs12074309	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12088941	0.96[EUR][1000 genomes]
rs12089658	0.84[EUR][1000 genomes]
rs12090246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12097169	0.86[EUR][1000 genomes]
rs16832976	0.81[AFR][1000 genomes]
rs34761930	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3892218	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59603391	0.94[EUR][1000 genomes]
rs61321900	0.86[EUR][1000 genomes]
rs6587556	0.89[AFR][1000 genomes]
rs7537292	0.82[AFR][1000 genomes];0.81[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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3399787	chr1:151104353-151106901	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
2	chr1:151079800-151114800	Weak transcription	HSMM	muscle
3	chr1:151103400-151106200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:151103400-151106400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:151103600-151106200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:151103600-151106200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr1:151104000-151114800	Weak transcription	Psoas Muscle	Psoas
8	chr1:151104200-151106200	Enhancers	Fetal Brain Male	brain
9	chr1:151104200-151107800	Weak transcription	Liver	Liver
10	chr1:151104400-151106200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:151104400-151106600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:151104400-151106800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:151104400-151107600	Weak transcription	GM12878-XiMat	blood
14	chr1:151104400-151110400	Weak transcription	NHLF	lung
15	chr1:151104400-151111200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
18	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
19	chr1:151104600-151106200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:151104600-151106200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:151104600-151106200	Weak transcription	Fetal Lung	lung
22	chr1:151104600-151106600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:151104600-151106600	Weak transcription	Brain Anterior Caudate	brain
24	chr1:151104600-151106600	Weak transcription	HUVEC	blood vessel
25	chr1:151104600-151107600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:151104600-151108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:151104600-151109000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
30	chr1:151104800-151106200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:151104800-151106600	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr1:151104800-151106800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:151104800-151107600	Weak transcription	Lung	lung
34	chr1:151104800-151108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:151104800-151108400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:151105000-151106200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:151105000-151114800	Strong transcription	Fetal Brain Female	brain
39	chr1:151105000-151114800	Weak transcription	Right Atrium	heart
40	chr1:151105000-151115400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:151105000-151115600	Weak transcription	Fetal Thymus	thymus
42	chr1:151105200-151106800	Weak transcription	Adipose Nuclei	Adipose
43	chr1:151105200-151108200	Weak transcription	Esophagus	oesophagus
44	chr1:151105200-151115200	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:151105200-151115400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
47	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:151105600-151106200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:151105600-151106400	Genic enhancers	Fetal Muscle Leg	muscle
50	chr1:151105600-151106600	Bivalent Enhancer	Fetal Stomach	stomach

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