Variant report

Variant	rs13243214
Chromosome Location	chr7:2817455-2817456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2797742..2801425-chr7:2817123..2820574,4	K562	blood:
2	chr7:2810442..2813051-chr7:2815246..2817707,2	K562	blood:
3	chr7:2816808..2818862-chr7:2824374..2826830,2	K562	blood:
4	chr7:2810431..2812589-chr7:2814723..2817684,2	K562	blood:
5	chr7:2815376..2818308-chr7:2821717..2825874,3	K562	blood:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1182172	0.84[EUR][1000 genomes]
rs1182174	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182176	0.86[EUR][1000 genomes]
rs1182177	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182178	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182179	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182181	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182182	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182183	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182184	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182185	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182186	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182187	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182188	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182189	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182198	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1182199	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1182207	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182208	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182209	0.91[ASN][1000 genomes]
rs1183085	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1636264	0.82[EUR][1000 genomes]
rs1713919	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2107964	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2158694	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248390	0.86[ASN][1000 genomes]
rs2251491	0.86[ASN][1000 genomes]
rs2260230	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266922	0.92[ASN][1000 genomes]
rs2283779	0.99[ASN][1000 genomes]
rs2283783	0.86[ASN][1000 genomes]
rs2283784	0.86[ASN][1000 genomes]
rs2527683	0.96[ASN][1000 genomes]
rs2527684	0.96[ASN][1000 genomes]
rs2527687	0.89[ASN][1000 genomes]
rs2527690	0.87[ASN][1000 genomes]
rs2527692	0.86[ASN][1000 genomes]
rs2527694	0.85[ASN][1000 genomes]
rs2527695	0.85[ASN][1000 genomes]
rs2527696	0.85[ASN][1000 genomes]
rs2533878	0.84[EUR][1000 genomes]
rs2533879	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2533882	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2533884	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2644274	0.86[ASN][1000 genomes]
rs2644275	0.86[ASN][1000 genomes]
rs2644294	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644295	0.84[ASN][1000 genomes]
rs2644296	0.85[ASN][1000 genomes]
rs2644297	0.85[ASN][1000 genomes]
rs2644298	0.85[ASN][1000 genomes]
rs2644312	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35957220	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6970963	0.93[ASN][1000 genomes]
rs6978692	0.86[ASN][1000 genomes]
rs709282	0.86[ASN][1000 genomes]
rs757791	0.81[ASN][1000 genomes]
rs7777484	0.95[ASN][1000 genomes]
rs7790322	0.83[AFR][1000 genomes]
rs7807978	0.95[ASN][1000 genomes]
rs798480	0.96[ASN][1000 genomes]
rs798481	0.80[ASN][1000 genomes]
rs798482	0.96[ASN][1000 genomes]
rs798485	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798486	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798487	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798488	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798489	0.89[EUR][1000 genomes]
rs798490	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798491	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798492	0.86[ASN][1000 genomes]
rs798493	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798494	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798495	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798496	0.85[EUR][1000 genomes]
rs798497	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798498	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798499	0.86[ASN][1000 genomes]
rs798500	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798502	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs798506	0.86[EUR][1000 genomes]
rs798508	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798511	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798512	0.86[ASN][1000 genomes]
rs798513	0.86[ASN][1000 genomes]
rs798514	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798518	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798526	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798528	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs798531	0.86[ASN][1000 genomes]
rs798536	0.80[ASN][1000 genomes]
rs798555	0.82[ASN][1000 genomes]
rs798557	0.82[ASN][1000 genomes]
rs798562	0.81[ASN][1000 genomes]
rs960273	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[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	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
6	nsv1032282	chr7:2789555-2820774	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	esv2761071	chr7:2811338-2822933	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13243214	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs13243214	GNA12	cis	Nerve Tibial	GTEx
rs13243214	GNA12	cis	Artery Tibial	GTEx
rs13243214	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
3	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:2798000-2827400	Weak transcription	Thymus	Thymus
5	chr7:2799200-2827200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:2799600-2825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:2800800-2818200	Weak transcription	Hela-S3	cervix
8	chr7:2801000-2827600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr7:2801000-2829600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:2801000-2831600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:2801000-2831600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:2802600-2826400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:2803200-2822600	Weak transcription	Right Ventricle	heart
14	chr7:2803400-2818000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:2803400-2818000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:2803400-2833400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:2803600-2820800	Weak transcription	Fetal Heart	heart
18	chr7:2803600-2822200	Weak transcription	HUVEC	blood vessel
19	chr7:2803600-2822600	Weak transcription	Left Ventricle	heart
20	chr7:2803600-2824200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:2803600-2826800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:2803800-2818200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:2803800-2821000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr7:2803800-2823800	Weak transcription	NH-A	brain
25	chr7:2803800-2824200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:2804400-2821200	Weak transcription	NHDF-Ad	bronchial
27	chr7:2804600-2818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:2807800-2827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
31	chr7:2811400-2824800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:2811600-2819800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:2811600-2824200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:2811800-2817800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:2811800-2820000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:2812400-2818200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:2812600-2818200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:2812600-2831400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:2812800-2817600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:2813200-2817800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:2813600-2821800	Weak transcription	GM12878-XiMat	blood
42	chr7:2813800-2821200	Weak transcription	Osteobl	bone
43	chr7:2813800-2825200	Weak transcription	HSMM	muscle
44	chr7:2813800-2829200	Weak transcription	Esophagus	oesophagus
45	chr7:2814000-2822600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr7:2814200-2818600	Weak transcription	NHLF	lung
47	chr7:2814200-2823800	Weak transcription	Lung	lung
48	chr7:2814400-2818000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:2814400-2838800	Weak transcription	K562	blood
50	chr7:2814600-2824200	Weak transcription	Fetal Kidney	kidney

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