Variant report

Variant	rs7309982
Chromosome Location	chr12:12550539-12550540
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:12549500..12552302-chr12:12715831..12718057,2	MCF-7	breast:
2	chr12:12550258..12553161-chr12:12554299..12558157,3	MCF-7	breast:
3	chr12:12549798..12552147-chr12:12868684..12871566,2	MCF-7	breast:
4	chr12:12546053..12553032-chr12:12712110..12718542,11	MCF-7	breast:
5	chr12:12548191..12550928-chr12:12559817..12561583,2	MCF-7	breast:
6	chr12:12547827..12551024-chr12:12713596..12715530,3	MCF-7	breast:
7	chr12:12550464..12553838-chr12:12621141..12625480,5	MCF-7	breast:
8	chr12:12549954..12552234-chr12:12764037..12766032,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction
ENSG00000111276	Chromatin interaction
ENSG00000111269	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1019340	0.84[JPT][hapmap]
rs1030069	0.83[JPT][hapmap]
rs10459098	0.84[JPT][hapmap]
rs10505765	0.83[ASN][1000 genomes]
rs10743982	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs10845539	0.84[JPT][hapmap]
rs10845545	0.83[JPT][hapmap]
rs10845546	0.83[JPT][hapmap]
rs11561172	0.83[JPT][hapmap]
rs11609375	0.84[JPT][hapmap]
rs11829916	0.82[ASN][1000 genomes]
rs16907990	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs16908006	0.83[GIH][hapmap]
rs16908059	0.81[CHD][hapmap]
rs16908062	0.81[CHD][hapmap]
rs16908076	0.81[CHD][hapmap]
rs16908101	0.81[CHD][hapmap]
rs2193269	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2193270	0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28853875	0.90[ASN][1000 genomes]
rs3925170	0.84[JPT][hapmap]
rs4763825	0.84[JPT][hapmap]
rs4763829	0.84[JPT][hapmap]
rs4763830	0.84[JPT][hapmap]
rs56089442	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56701819	0.84[ASN][1000 genomes]
rs56796062	0.90[ASN][1000 genomes]
rs56915387	0.82[ASN][1000 genomes]
rs57348917	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61543155	0.83[ASN][1000 genomes]
rs6488520	0.84[JPT][hapmap];0.83[TSI][hapmap]
rs6488527	0.83[GIH][hapmap]
rs7135655	0.93[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7295080	0.84[JPT][hapmap]
rs7300150	0.91[ASN][1000 genomes]
rs73061463	0.82[ASN][1000 genomes]
rs7309503	0.84[JPT][hapmap]
rs7310012	0.83[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7311363	0.87[ASN][1000 genomes]
rs7311364	0.84[JPT][hapmap]
rs7313825	0.84[JPT][hapmap]
rs73283441	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953025	0.84[JPT][hapmap]
rs7967111	0.84[JPT][hapmap]
rs7967230	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7967466	0.89[JPT][hapmap]
rs7969849	0.84[JPT][hapmap]
rs7980390	0.83[GIH][hapmap]
rs888198	0.88[ASW][hapmap]
rs888200	0.84[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7309982	GPRC5D	cis	parietal	SCAN
rs7309982	PRH1	cis	parietal	SCAN
rs7309982	EPS8	cis	cerebellum	SCAN
rs7309982	MAGOHB	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
5	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
9	chr12:12538200-12551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:12538400-12551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:12538400-12552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:12538400-12555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:12538800-12551400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:12540800-12550800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:12540800-12551000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:12540800-12553800	Weak transcription	GM12878-XiMat	blood
21	chr12:12540800-12555400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:12541000-12550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:12541000-12551000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:12541000-12551000	Weak transcription	Small Intestine	intestine
25	chr12:12541400-12550800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:12541400-12552600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
28	chr12:12541800-12557200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:12542800-12551600	Weak transcription	Lung	lung
30	chr12:12543000-12558800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:12545800-12555200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:12545800-12555200	Weak transcription	Fetal Intestine Small	intestine
33	chr12:12546000-12551400	Weak transcription	Fetal Intestine Large	intestine
34	chr12:12546000-12553200	Weak transcription	Right Atrium	heart
35	chr12:12546000-12556400	Weak transcription	K562	blood
36	chr12:12546200-12551400	Weak transcription	Left Ventricle	heart
37	chr12:12546200-12551400	Weak transcription	Pancreas	Pancrea
38	chr12:12547200-12556000	Weak transcription	Fetal Thymus	thymus
39	chr12:12547600-12551000	Weak transcription	Stomach Mucosa	stomach
40	chr12:12547600-12553400	Enhancers	Brain Substantia Nigra	brain
41	chr12:12547600-12555400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:12548000-12551200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:12548600-12551000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:12548600-12553400	Enhancers	Brain Anterior Caudate	brain
45	chr12:12548600-12553400	Enhancers	Brain Hippocampus Middle	brain
46	chr12:12548600-12554200	Enhancers	HepG2	liver
47	chr12:12548800-12551400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:12549200-12550600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:12549200-12552200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:12549200-12552400	Enhancers	NHLF	lung

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