Variant report

Variant	rs12818390
Chromosome Location	chr12:31832544-31832545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31832533..31834695-chr12:32259556..32261567,2	K562	blood:

Variant related genes	Relation type
ENSG00000151746	Chromatin interaction
ENSG00000257530	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1072778	0.92[CEU][hapmap]
rs11051544	0.83[ASW][hapmap];0.88[CHD][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12303424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374171	0.92[CEU][hapmap]
rs2388926	0.92[CEU][hapmap]
rs7295568	0.92[CEU][hapmap]
rs7968269	0.84[CEU][hapmap]
rs7968792	0.92[CEU][hapmap];0.86[MKK][hapmap]
rs7971803	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7980264	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers 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 target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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 target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12818390	REP15	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31813200-31837000	Weak transcription	Fetal Brain Male	brain
2	chr12:31813400-31835200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:31813400-31835600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:31813400-31836200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:31815200-31840600	Weak transcription	Pancreas	Pancrea
6	chr12:31817400-31850400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:31822400-31835600	Weak transcription	Fetal Lung	lung
8	chr12:31822400-31836600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:31822400-31840600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:31822600-31835200	Weak transcription	Ovary	ovary
11	chr12:31822600-31835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:31822600-31835600	Weak transcription	Fetal Brain Female	brain
13	chr12:31822600-31835600	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:31822600-31836000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:31822600-31836400	Weak transcription	Brain Anterior Caudate	brain
16	chr12:31822600-31862000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
18	chr12:31822800-31834800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:31822800-31835000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:31822800-31835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:31822800-31835600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:31822800-31835600	Weak transcription	Dnd41	blood
23	chr12:31823000-31835400	Weak transcription	Fetal Intestine Small	intestine
24	chr12:31823400-31835600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:31823600-31835200	Weak transcription	Thymus	Thymus
26	chr12:31823800-31836200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:31824600-31835600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:31824800-31834800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:31824800-31835000	Weak transcription	Fetal Thymus	thymus
30	chr12:31824800-31835400	Weak transcription	Primary B cells from cord blood	blood
31	chr12:31824800-31835600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:31825400-31835200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:31826800-31836200	Weak transcription	Brain Substantia Nigra	brain
34	chr12:31827000-31835200	Weak transcription	Primary T cells from cord blood	blood
35	chr12:31827000-31835200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:31827000-31835400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:31827000-31835600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:31827000-31871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:31827400-31835600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:31827400-31855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:31827800-31835200	Weak transcription	Liver	Liver
42	chr12:31828200-31835200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:31828200-31835600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:31828800-31835200	Weak transcription	Fetal Stomach	stomach
45	chr12:31828800-31835600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:31828800-31836000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:31831000-31835000	Weak transcription	Hela-S3	cervix
48	chr12:31831200-31835600	Weak transcription	A549	lung
49	chr12:31831400-31835400	Weak transcription	Brain Germinal Matrix	brain
50	chr12:31832200-31833000	Strong transcription	Primary B cells from peripheral blood	blood

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