Variant report

Variant	rs12747807
Chromosome Location	chr1:227343741-227343742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227126988..227128747-chr1:227341911..227344210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10495259	0.82[EUR][1000 genomes]
rs11585910	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11586575	0.81[EUR][1000 genomes]
rs12118022	0.87[EUR][1000 genomes]
rs12119153	0.84[AFR][1000 genomes]
rs12119448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12121729	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12123597	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12127665	0.82[EUR][1000 genomes]
rs12128667	0.82[EUR][1000 genomes]
rs12131061	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12131913	0.82[EUR][1000 genomes]
rs12131933	0.84[AFR][1000 genomes]
rs12134379	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12136857	0.82[EUR][1000 genomes]
rs12138383	1.00[AFR][1000 genomes]
rs12141838	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12739480	0.84[EUR][1000 genomes]
rs12744825	0.82[EUR][1000 genomes]
rs12751015	0.82[EUR][1000 genomes]
rs12752546	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1513607	0.84[AFR][1000 genomes]
rs17545704	0.82[EUR][1000 genomes]
rs17546688	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17613235	1.00[AFR][1000 genomes]
rs2063661	0.84[AFR][1000 genomes]
rs34113967	0.84[AFR][1000 genomes]
rs34169114	0.82[EUR][1000 genomes]
rs35156994	0.82[EUR][1000 genomes]
rs35672262	0.93[EUR][1000 genomes]
rs36133891	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3738727	0.88[EUR][1000 genomes]
rs4263966	0.82[EUR][1000 genomes]
rs4308948	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61834324	0.84[AFR][1000 genomes]
rs61836468	0.82[EUR][1000 genomes]
rs6660168	1.00[AFR][1000 genomes]
rs6664330	0.81[EUR][1000 genomes]
rs6675572	1.00[AFR][1000 genomes]
rs7512871	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
2	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
3	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
6	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:227316600-227352200	Weak transcription	Gastric	stomach
8	chr1:227317000-227374200	Weak transcription	HepG2	liver
9	chr1:227323200-227346400	Weak transcription	Brain Substantia Nigra	brain
10	chr1:227324200-227348400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:227326600-227355200	Weak transcription	Small Intestine	intestine
12	chr1:227327000-227346200	Weak transcription	NH-A	brain
13	chr1:227327000-227346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:227327000-227347600	Weak transcription	Fetal Heart	heart
15	chr1:227327200-227348200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:227327200-227348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:227328000-227354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:227328400-227350000	Weak transcription	Fetal Brain Male	brain
19	chr1:227328600-227351600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:227328800-227346200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:227328800-227354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:227329600-227358400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
24	chr1:227329800-227348400	Weak transcription	Fetal Brain Female	brain
25	chr1:227331400-227346200	Weak transcription	Pancreas	Pancrea
26	chr1:227331600-227355000	Weak transcription	Brain Anterior Caudate	brain
27	chr1:227331600-227358400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:227332200-227345800	Weak transcription	Fetal Stomach	stomach
29	chr1:227332400-227347400	Weak transcription	Fetal Intestine Small	intestine
30	chr1:227332800-227345800	Weak transcription	Left Ventricle	heart
31	chr1:227332800-227346000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:227332800-227346200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:227332800-227346200	Weak transcription	NHEK	skin
34	chr1:227332800-227346400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:227332800-227346400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:227332800-227350000	Weak transcription	HMEC	breast
37	chr1:227332800-227350200	Weak transcription	Lung	lung
38	chr1:227332800-227354600	Weak transcription	Ovary	ovary
39	chr1:227333000-227346000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:227333000-227346600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:227333000-227349400	Weak transcription	Placenta	Placenta
42	chr1:227333200-227354800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:227333400-227344400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:227333400-227344400	Weak transcription	NHDF-Ad	bronchial
45	chr1:227333400-227344600	Weak transcription	HSMM	muscle
46	chr1:227333400-227345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:227333400-227346000	Weak transcription	Fetal Lung	lung
48	chr1:227333400-227346200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:227333400-227346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:227333400-227346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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