Variant report

Variant	rs12320537
Chromosome Location	chr12:58021091-58021092
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57984885..57986845-chr12:58019565..58021486,2	MCF-7	breast:
2	chr12:57978631..57980822-chr12:58019393..58022185,2	MCF-7	breast:
3	chr12:58015842..58017854-chr12:58020361..58022669,3	MCF-7	breast:
4	chr12:58013181..58015387-chr12:58019093..58021803,2	MCF-7	breast:
5	chr12:57912625..57915071-chr12:58019101..58021817,3	K562	blood:
6	chr12:57912625..57916215-chr12:58016074..58021603,6	K562	blood:

Variant related genes	Relation type
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11172290	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12304013	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12318458	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12322482	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2258877	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277323	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2619468	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619469	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2619470	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2640607	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34919374	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35831868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3899676	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71432310	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715930	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774896	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774897	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774898	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774899	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58015600-58021400	Weak transcription	Gastric	stomach
2	chr12:58016000-58021200	Weak transcription	Pancreas	Pancrea
3	chr12:58016200-58021400	Weak transcription	Right Ventricle	heart
4	chr12:58017000-58025000	Weak transcription	K562	blood
5	chr12:58018000-58024600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:58018600-58023000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:58018800-58021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:58018800-58024000	Strong transcription	Brain Germinal Matrix	brain
9	chr12:58018800-58024200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:58019000-58023400	Weak transcription	Brain Angular Gyrus	brain
11	chr12:58019000-58023400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:58019200-58021600	Strong transcription	Fetal Brain Female	brain
13	chr12:58019200-58022000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr12:58019400-58025200	Weak transcription	Hela-S3	cervix
15	chr12:58019600-58022200	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr12:58020000-58021800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:58020000-58022600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:58020200-58021400	Weak transcription	Spleen	Spleen
19	chr12:58020200-58021800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
20	chr12:58020400-58021200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:58020400-58021600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:58020400-58024800	Weak transcription	HepG2	liver
23	chr12:58020600-58021400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr12:58020600-58021400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr12:58020600-58021400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:58020600-58022200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr12:58020600-58022200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:58020600-58022600	Bivalent Enhancer	Placenta	Placenta
29	chr12:58020600-58024800	Strong transcription	A549	lung
30	chr12:58020600-58026200	Weak transcription	Aorta	Aorta
31	chr12:58020800-58021200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
32	chr12:58020800-58021200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
33	chr12:58020800-58021200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr12:58020800-58022000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
35	chr12:58020800-58022000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:58020800-58025200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:58021000-58021200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:58021000-58021400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr12:58021000-58022200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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