Variant report

Variant	rs12230111
Chromosome Location	chr12:57822616-57822617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57821571-57823060	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:57821228-57824428	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
2	chr12:57664699..57666780-chr12:57821580..57823850,2	K562	blood:
3	chr12:57672368..57674775-chr12:57822497..57825097,2	K562	blood:
4	chr12:57821945..57826454-chr12:57843844..57847049,4	K562	blood:
5	chr12:57685797..57688003-chr12:57821497..57823959,2	K562	blood:
6	chr12:57822102..57825804-chr12:57846903..57851131,6	MCF-7	breast:
7	chr12:57734038..57735691-chr12:57822012..57824605,2	MCF-7	breast:
8	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258001	TF binding region
ENSG00000139269	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000111087	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10783823	0.89[ASN][1000 genomes]
rs10876976	0.84[EUR][1000 genomes]
rs10876977	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876978	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876980	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876981	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876983	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172165	0.84[ASN][1000 genomes]
rs11172170	0.84[ASN][1000 genomes]
rs11172190	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172191	0.83[EUR][1000 genomes]
rs11172205	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172211	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172214	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172222	0.85[EUR][1000 genomes]
rs12423654	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12579911	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1284252	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798710	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063778	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2280139	0.86[EUR][1000 genomes]
rs28504983	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4108243	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760228	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760236	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760244	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760305	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760306	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760356	0.84[ASN][1000 genomes]
rs4760357	0.82[ASN][1000 genomes]
rs481196	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs491750	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492749	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512223	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs533975	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537482	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs543410	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560048	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs568793	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs575153	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581136	0.83[ASN][1000 genomes]
rs6581139	0.90[ASN][1000 genomes]
rs7132367	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303070	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7307059	0.84[ASN][1000 genomes]
rs7309659	0.86[ASN][1000 genomes]
rs7398058	0.84[ASN][1000 genomes]
rs7980310	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9738004	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57753200-57823800	Weak transcription	Esophagus	oesophagus
2	chr12:57770800-57824000	Weak transcription	Gastric	stomach
3	chr12:57780800-57823200	Weak transcription	Spleen	Spleen
4	chr12:57783800-57823200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:57788600-57823200	Weak transcription	NHDF-Ad	bronchial
6	chr12:57789200-57823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:57789400-57823200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:57790000-57823200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:57795400-57823000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:57795400-57823200	Weak transcription	Adipose Nuclei	Adipose
11	chr12:57795400-57823200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:57795400-57823200	Weak transcription	HMEC	breast
13	chr12:57795400-57823600	Weak transcription	Aorta	Aorta
14	chr12:57795800-57823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:57795800-57823200	Weak transcription	Right Ventricle	heart
16	chr12:57808000-57823000	Weak transcription	NH-A	brain
17	chr12:57809400-57823000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:57809400-57823200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:57809600-57822800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:57809600-57823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:57809600-57823200	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:57809600-57823400	Weak transcription	Fetal Kidney	kidney
23	chr12:57809800-57823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:57810200-57823400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:57810200-57823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:57811200-57823000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:57811400-57822800	Weak transcription	A549	lung
28	chr12:57812000-57822800	Weak transcription	Hela-S3	cervix
29	chr12:57812000-57823200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:57812200-57823200	Weak transcription	Brain Anterior Caudate	brain
31	chr12:57812200-57823200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:57812200-57823200	Weak transcription	Ovary	ovary
33	chr12:57812600-57822800	Weak transcription	Right Atrium	heart
34	chr12:57812600-57823200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:57812600-57823200	Weak transcription	Pancreas	Pancrea
36	chr12:57812600-57823200	Weak transcription	HSMMtube	muscle
37	chr12:57813000-57823200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:57814000-57823200	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:57814600-57822800	Weak transcription	K562	blood
40	chr12:57814600-57823000	Weak transcription	HUVEC	blood vessel
41	chr12:57814800-57822800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:57814800-57823200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:57815000-57823000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:57815000-57823200	Weak transcription	Colonic Mucosa	Colon
45	chr12:57815000-57823200	Weak transcription	Psoas Muscle	Psoas
46	chr12:57815200-57823200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:57815600-57823200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr12:57816600-57822800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:57816600-57822800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:57816600-57823000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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