Variant report

Variant	rs2533889
Chromosome Location	chr7:2900309-2900310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2899669..2908273-chr7:2908845..2917311,19	MCF-7	breast:
2	chr7:2840989..2843373-chr7:2899244..2901944,2	MCF-7	breast:
3	chr7:2898176..2901169-chr7:2925021..2926702,2	MCF-7	breast:
4	chr7:2899154..2902095-chr7:2911868..2915224,3	MCF-7	breast:
5	chr7:2897460..2900417-chr7:2901326..2905406,6	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1182151	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1182155	0.88[EUR][1000 genomes]
rs1182156	0.97[ASN][1000 genomes]
rs11973498	0.82[EUR][1000 genomes]
rs12700373	0.82[EUR][1000 genomes]
rs13230946	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13230995	0.82[EUR][1000 genomes]
rs1614791	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1623138	0.96[ASN][1000 genomes]
rs1636247	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1636249	0.82[EUR][1000 genomes]
rs1636250	0.81[EUR][1000 genomes]
rs1636253	0.82[EUR][1000 genomes]
rs1636254	0.82[EUR][1000 genomes]
rs1636255	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1636256	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1639036	0.82[EUR][1000 genomes]
rs1639040	0.82[EUR][1000 genomes]
rs1639064	0.88[ASN][1000 genomes]
rs1639065	0.81[ASN][1000 genomes]
rs1639066	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1713912	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1713913	0.91[ASN][1000 genomes]
rs2527677	0.82[EUR][1000 genomes]
rs2527680	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2527681	0.84[EUR][1000 genomes]
rs2533867	0.81[EUR][1000 genomes]
rs2533868	0.81[EUR][1000 genomes]
rs2533870	0.82[EUR][1000 genomes]
rs2533871	0.81[EUR][1000 genomes]
rs2533877	0.82[EUR][1000 genomes]
rs2533878	0.81[EUR][1000 genomes]
rs2533891	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2644281	0.82[EUR][1000 genomes]
rs2644286	0.82[EUR][1000 genomes]
rs2644293	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2644300	0.82[EUR][1000 genomes]
rs2644309	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71522301	0.82[EUR][1000 genomes]
rs71522302	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71524003	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7783400	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv887315	chr7:2895627-2935424	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1022938	chr7:2899514-3131881	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2533889	GNA12	cis	Artery Tibial	GTEx
rs2533889	GNA12	cis	Nerve Tibial	GTEx
rs2533889	GNA12	cis	multi-tissue	Pritchard
rs2533889	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2884600-2902800	Weak transcription	Right Ventricle	heart
2	chr7:2885000-2902000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:2891600-2902000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:2891600-2902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr7:2891600-2902800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:2892800-2902000	Weak transcription	NHLF	lung
8	chr7:2893200-2902000	Weak transcription	Ovary	ovary
9	chr7:2893400-2902600	Weak transcription	GM12878-XiMat	blood
10	chr7:2895800-2902800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:2897400-2902800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:2897600-2902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:2897600-2902200	Weak transcription	Placenta	Placenta
14	chr7:2898400-2900400	Enhancers	Fetal Muscle Leg	muscle
15	chr7:2898800-2902800	Weak transcription	HSMMtube	muscle
16	chr7:2898800-2903200	Weak transcription	Thymus	Thymus
17	chr7:2899400-2902600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:2899800-2900800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:2900000-2900800	Enhancers	Fetal Muscle Trunk	muscle
20	chr7:2900000-2902800	Weak transcription	Pancreas	Pancrea
21	chr7:2900200-2900400	Enhancers	K562	blood
22	chr7:2900200-2900600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:2900200-2900600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:2900200-2900600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr7:2900200-2900600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:2900200-2900600	Enhancers	Brain Anterior Caudate	brain
27	chr7:2900200-2900600	Enhancers	Brain Germinal Matrix	brain
28	chr7:2900200-2900600	Enhancers	Brain Hippocampus Middle	brain
29	chr7:2900200-2900600	Enhancers	Fetal Brain Female	brain
30	chr7:2900200-2900600	Enhancers	Fetal Intestine Small	intestine
31	chr7:2900200-2900600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr7:2900200-2900600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr7:2900200-2900600	Flanking Active TSS	HepG2	liver
34	chr7:2900200-2900600	Enhancers	HMEC	breast
35	chr7:2900200-2900600	Enhancers	HSMM	muscle
36	chr7:2900200-2900800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:2900200-2900800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:2900200-2900800	Enhancers	Duodenum Mucosa	Duodenum
39	chr7:2900200-2900800	Enhancers	NH-A	brain
40	chr7:2900200-2900800	Enhancers	NHEK	skin
41	chr7:2900200-2901200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:2900200-2901400	Enhancers	Stomach Mucosa	stomach
43	chr7:2900200-2902200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:2900200-2902600	Weak transcription	Gastric	stomach
45	chr7:2900200-2902600	Weak transcription	Small Intestine	intestine

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