Variant report

Variant	rs798520
Chromosome Location	chr7:2776627-2776628
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2770258..2772875-chr7:2776418..2779322,2	MCF-7	breast:
2	chr7:2775731..2778086-chr7:2883079..2885342,2	MCF-7	breast:
3	chr7:2776568..2779036-chr7:2798696..2800622,2	MCF-7	breast:
4	chr7:2768256..2774537-chr7:2775031..2780281,7	K562	blood:
5	chr7:2756196..2760316-chr7:2775723..2779597,5	K562	blood:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1182206	0.84[EUR][1000 genomes]
rs208346	0.91[ASN][1000 genomes]
rs208356	0.97[ASN][1000 genomes]
rs2251718	0.80[ASN][1000 genomes]
rs2255541	0.80[ASN][1000 genomes]
rs2255782	0.80[ASN][1000 genomes]
rs2258960	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2266923	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527682	0.81[EUR][1000 genomes]
rs2644276	0.80[ASN][1000 genomes]
rs2693566	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846992	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs709280	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709281	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs757789	0.81[ASN][1000 genomes]
rs757790	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798501	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798504	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798505	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs798509	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798515	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798516	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798517	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798519	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798521	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798523	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798524	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798525	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798527	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798529	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798530	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1017611	chr7:2750418-2781716	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv538654	chr7:2750418-2781716	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	nsv605872	chr7:2770899-2776698	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs798520	GNA12	cis	Artery Tibial	GTEx
rs798520	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
3	chr7:2761000-2796200	Weak transcription	Hela-S3	cervix
4	chr7:2761000-2797000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:2771000-2780400	Weak transcription	Aorta	Aorta
6	chr7:2771200-2777400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:2771200-2779400	Enhancers	Primary hematopoietic stem cells	blood
8	chr7:2771200-2782200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:2771200-2783200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:2771200-2796200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:2771400-2780600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:2771400-2782400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:2771400-2785000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:2771400-2796200	Weak transcription	NHEK	skin
15	chr7:2771600-2777800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:2771600-2781800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:2772000-2776800	Enhancers	Right Atrium	heart
18	chr7:2772200-2776800	Enhancers	Left Ventricle	heart
19	chr7:2772400-2780400	Weak transcription	HMEC	breast
20	chr7:2772600-2776800	Enhancers	Fetal Heart	heart
21	chr7:2772600-2777000	Enhancers	Fetal Muscle Leg	muscle
22	chr7:2772800-2776800	Enhancers	Brain Anterior Caudate	brain
23	chr7:2772800-2783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:2773000-2776800	Genic enhancers	Fetal Stomach	stomach
25	chr7:2773200-2776800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:2773200-2778800	Enhancers	Primary B cells from peripheral blood	blood
27	chr7:2773200-2782400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:2773200-2783200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:2773200-2796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:2773200-2796400	Weak transcription	NH-A	brain
31	chr7:2773200-2797000	Weak transcription	Pancreas	Pancrea
32	chr7:2773400-2776800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:2773600-2776800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:2773600-2777800	Weak transcription	Stomach Mucosa	stomach
35	chr7:2773600-2778600	Enhancers	Primary B cells from cord blood	blood
36	chr7:2773600-2796400	Weak transcription	Osteobl	bone
37	chr7:2774000-2777000	Enhancers	Fetal Thymus	thymus
38	chr7:2774800-2776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:2774800-2778000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr7:2774800-2778200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:2775000-2781600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:2775200-2777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:2775200-2778000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:2775200-2778000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr7:2775200-2781400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr7:2775200-2783200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:2775200-2783200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr7:2775200-2790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:2775200-2791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:2775200-2796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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