Variant report

Variant	rs12304941
Chromosome Location	chr12:76102133-76102134
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:76101462..76103628-chr12:76173013..76174692,2	MCF-7	breast:
2	chr12:76102037..76104133-chr12:76105458..76107815,2	K562	blood:
3	chr12:76101934..76108267-chr12:76336185..76339499,5	MCF-7	breast:
4	chr12:76101957..76104575-chr12:76208488..76210993,2	MCF-7	breast:
5	chr12:76100797..76102905-chr12:76103958..76106069,2	K562	blood:
6	chr12:76092093..76110851-chr12:76415034..76433496,122	MCF-7	breast:
7	chr12:76098446..76100870-chr12:76101330..76106018,5	K562	blood:
8	chr12:76102097..76104624-chr12:76369876..76371857,2	MCF-7	breast:
9	chr12:76097180..76098838-chr12:76099370..76102152,2	MCF-7	breast:
10	chr12:76098446..76100265-chr12:76101330..76104359,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257839	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10785202	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10785206	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180648	0.91[AMR][1000 genomes]
rs11180650	0.90[JPT][hapmap]
rs12309589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422374	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882020	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1920415	0.98[ASN][1000 genomes]
rs4300421	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4578425	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59472164	0.91[AMR][1000 genomes]
rs6582296	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7295963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309950	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310061	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73363702	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7959975	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs7960787	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7964632	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7980070	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][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	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv899314	chr12:76079814-76110751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12304941	FLJ43390	trans	lymphoblastoid	seeQTL
rs12304941	ANO3	trans	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76098200-76104000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:76098400-76104600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:76098400-76105200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:76098800-76104600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:76098800-76105000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:76098800-76114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:76098800-76114400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:76099200-76102200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:76099600-76110800	Enhancers	HepG2	liver
10	chr12:76099800-76103000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:76099800-76103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:76100000-76106800	Weak transcription	Right Ventricle	heart
13	chr12:76100000-76115200	Weak transcription	Pancreas	Pancrea
14	chr12:76100200-76104600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:76100400-76104600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:76100400-76104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:76100400-76105400	Weak transcription	Psoas Muscle	Psoas
18	chr12:76100400-76106800	Weak transcription	Right Atrium	heart
19	chr12:76100400-76108400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:76100600-76103200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:76100600-76105400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:76100800-76102200	Enhancers	Osteobl	bone
23	chr12:76100800-76102600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:76100800-76102800	Weak transcription	Fetal Kidney	kidney
25	chr12:76100800-76103400	Weak transcription	Aorta	Aorta
26	chr12:76100800-76104000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:76100800-76104600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:76100800-76104800	Enhancers	HUVEC	blood vessel
29	chr12:76100800-76105000	Enhancers	NHDF-Ad	bronchial
30	chr12:76100800-76107000	Weak transcription	Small Intestine	intestine
31	chr12:76101000-76102200	Enhancers	K562	blood
32	chr12:76101000-76102600	Weak transcription	Fetal Lung	lung
33	chr12:76101000-76102600	Weak transcription	A549	lung
34	chr12:76101000-76103000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:76101000-76103400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:76101000-76103400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:76101000-76103600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:76101000-76103600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:76101000-76104200	Weak transcription	HMEC	breast
40	chr12:76101000-76104600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:76101000-76104800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:76101000-76105200	Weak transcription	Stomach Mucosa	stomach
43	chr12:76101000-76106000	Weak transcription	Dnd41	blood
44	chr12:76101000-76106000	Weak transcription	NH-A	brain
45	chr12:76101000-76113600	Weak transcription	Fetal Stomach	stomach
46	chr12:76101400-76103400	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:76101400-76103600	Weak transcription	NHEK	skin
48	chr12:76101400-76114200	Weak transcription	Left Ventricle	heart
49	chr12:76101400-76114800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:76101600-76102600	Weak transcription	Fetal Heart	heart

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