Variant report

Variant	rs12230536
Chromosome Location	chr12:65021153-65021154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr12:65021072-65021177	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:65019020..65021619-chr12:65065192..65067422,3	MCF-7	breast:
2	chr12:65019301..65021176-chr12:65062867..65064609,2	K562	blood:
3	chr12:65010556..65012937-chr12:65017376..65021348,4	K562	blood:
4	chr12:65018029..65021346-chr12:65072247..65076410,6	MCF-7	breast:
5	chr12:65013056..65015741-chr12:65019440..65021647,2	MCF-7	breast:
6	chr12:64844472..64846840-chr12:65019435..65021283,2	MCF-7	breast:
7	chr12:65001678..65008078-chr12:65013108..65023657,17	MCF-7	breast:
8	chr12:65008925..65011325-chr12:65018761..65021697,3	MCF-7	breast:
9	chr12:65019590..65021389-chr12:65024467..65026055,3	K562	blood:
10	chr12:65001526..65007900-chr12:65015799..65021807,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225195	TF binding region
ENSG00000153179	Chromatin interaction
ENSG00000183735	Chromatin interaction
ENSG00000256670	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1008159	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1008160	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11175470	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175471	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175481	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175497	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175509	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11837759	0.85[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12814316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12816847	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824246	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12829878	0.85[CEU][hapmap]
rs12830436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12831875	0.85[CEU][hapmap]
rs17223244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17223391	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17823442	0.85[CEU][hapmap]
rs2078398	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35512928	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35674528	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35705715	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35860561	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1048199	chr12:64951666-65021700	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv541512	chr12:64951666-65021700	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv438218	chr12:65017844-65037483	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65006800-65031800	Weak transcription	Dnd41	blood
2	chr12:65010000-65023200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:65010800-65022200	Weak transcription	Spleen	Spleen
4	chr12:65018000-65021200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:65018000-65024600	Weak transcription	Aorta	Aorta
6	chr12:65018400-65029200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:65018600-65024800	Weak transcription	Gastric	stomach
8	chr12:65018600-65035000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:65019400-65024800	Weak transcription	Right Ventricle	heart
10	chr12:65019600-65021200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:65019600-65021200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:65019600-65021200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr12:65019600-65021600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr12:65019600-65022400	Enhancers	NHDF-Ad	bronchial
15	chr12:65019600-65027800	Weak transcription	Pancreas	Pancrea
16	chr12:65019800-65021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:65019800-65021200	Weak transcription	Stomach Mucosa	stomach
18	chr12:65019800-65021200	Enhancers	HepG2	liver
19	chr12:65019800-65021200	Weak transcription	HSMM	muscle
20	chr12:65019800-65021200	Weak transcription	NH-A	brain
21	chr12:65019800-65021400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr12:65019800-65021400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:65019800-65021600	Enhancers	Primary T cells from cord blood	blood
24	chr12:65019800-65022000	Enhancers	Colon Smooth Muscle	Colon
25	chr12:65019800-65022200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:65019800-65022200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:65019800-65022200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:65019800-65022400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:65019800-65022400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:65019800-65022600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:65019800-65022800	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:65019800-65022800	Weak transcription	Thymus	Thymus
33	chr12:65019800-65023000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:65019800-65023000	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:65019800-65024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:65019800-65024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:65019800-65025800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:65019800-65025800	Weak transcription	Fetal Lung	lung
39	chr12:65019800-65025800	Weak transcription	Psoas Muscle	Psoas
40	chr12:65019800-65026200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:65019800-65026400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:65019800-65026600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:65019800-65028400	Weak transcription	Colonic Mucosa	Colon
44	chr12:65019800-65028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:65019800-65029200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:65019800-65030600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:65019800-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:65020000-65021200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:65020000-65021200	Weak transcription	Adipose Nuclei	Adipose
50	chr12:65020000-65021400	Enhancers	Primary T helper cells fromperipheralblood	blood

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