Variant report

Variant	rs12307952
Chromosome Location	chr12:56358066-56358067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56348195..56352007-chr12:56357444..56361194,9	MCF-7	breast:
2	chr12:56319178..56327497-chr12:56356755..56363470,19	MCF-7	breast:
3	chr12:56357404..56359023-chr12:56359064..56360959,2	MCF-7	breast:
4	chr12:56137714..56140365-chr12:56357823..56359746,2	K562	blood:
5	chr12:56357871..56361008-chr12:56510432..56513466,3	K562	blood:
6	chr12:56357334..56358915-chr12:56360471..56362564,2	K562	blood:

Variant related genes	Relation type
ENSG00000139641	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11171705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2069391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2069398	0.98[EUR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12307952	PMEL	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56345400-56359000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56346600-56360000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:56346800-56359400	Weak transcription	Brain Anterior Caudate	brain
4	chr12:56347000-56359600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:56347200-56360000	Weak transcription	HSMMtube	muscle
6	chr12:56347400-56359600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:56347400-56359800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:56347400-56359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:56347600-56359800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:56347800-56359400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:56348200-56359400	Weak transcription	Liver	Liver
12	chr12:56348200-56359600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:56348200-56360000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:56348400-56359600	Weak transcription	Primary B cells from cord blood	blood
15	chr12:56348400-56359600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:56348400-56359800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:56348400-56359800	Weak transcription	Fetal Lung	lung
18	chr12:56348800-56359600	Weak transcription	Spleen	Spleen
19	chr12:56349200-56359600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:56349200-56359600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:56349400-56359400	Weak transcription	Dnd41	blood
22	chr12:56349400-56359600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:56349400-56359600	Weak transcription	Thymus	Thymus
24	chr12:56349600-56359400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:56349600-56359600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:56349800-56359600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:56350000-56359800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:56351200-56359200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:56351200-56359200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:56351600-56359800	Weak transcription	Primary T cells from cord blood	blood
31	chr12:56351800-56359200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:56351800-56359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:56351800-56359800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:56351800-56359800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:56351800-56359800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:56352000-56359600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:56352000-56359800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:56352200-56359200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:56352200-56359400	Weak transcription	Stomach Mucosa	stomach
40	chr12:56352400-56359000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:56352400-56359000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:56352600-56359000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:56352800-56359600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:56353000-56358800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr12:56353200-56359200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:56354000-56359800	Weak transcription	K562	blood
47	chr12:56354200-56359600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:56354400-56359400	Weak transcription	Ovary	ovary
49	chr12:56355400-56359000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:56355400-56359600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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