Variant report

Variant	rs2644294
Chromosome Location	chr7:2823476-2823477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2795883..2797584-chr7:2821948..2824040,2	K562	blood:
2	chr7:2820643..2823632-chr7:2824452..2826703,2	K562	blood:
3	chr7:2815376..2818308-chr7:2821717..2825874,3	K562	blood:
4	chr7:2822854..2825744-chr7:2825933..2828348,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1182172	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1182174	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182176	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182177	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182178	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182179	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182181	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182182	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182183	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1182184	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182185	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182186	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1182187	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182188	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1182189	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1182196	0.80[ASN][1000 genomes]
rs1182198	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1182199	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1182207	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1182208	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182209	0.87[ASN][1000 genomes]
rs1183085	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13243214	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636264	0.83[EUR][1000 genomes]
rs1713919	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2107964	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2158694	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2248390	0.88[ASN][1000 genomes]
rs2251491	0.88[ASN][1000 genomes]
rs2260230	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2266922	0.96[ASN][1000 genomes]
rs2283779	0.95[ASN][1000 genomes]
rs2283783	0.88[ASN][1000 genomes]
rs2283784	0.88[ASN][1000 genomes]
rs2527683	1.00[ASN][1000 genomes]
rs2527684	1.00[ASN][1000 genomes]
rs2527687	0.91[ASN][1000 genomes]
rs2527690	0.89[ASN][1000 genomes]
rs2527692	0.88[ASN][1000 genomes]
rs2527694	0.87[ASN][1000 genomes]
rs2527695	0.87[ASN][1000 genomes]
rs2527696	0.87[ASN][1000 genomes]
rs2533878	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2533879	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2533882	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2533884	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2644274	0.88[ASN][1000 genomes]
rs2644275	0.88[ASN][1000 genomes]
rs2644295	0.86[ASN][1000 genomes]
rs2644296	0.87[ASN][1000 genomes]
rs2644297	0.87[ASN][1000 genomes]
rs2644298	0.87[ASN][1000 genomes]
rs2644312	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35957220	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6970963	0.95[ASN][1000 genomes]
rs6978692	0.88[ASN][1000 genomes]
rs709282	0.82[ASN][1000 genomes]
rs757791	0.83[ASN][1000 genomes]
rs7777484	0.91[ASN][1000 genomes]
rs7790322	0.83[AFR][1000 genomes]
rs7807978	0.91[ASN][1000 genomes]
rs798480	0.91[ASN][1000 genomes]
rs798482	0.91[ASN][1000 genomes]
rs798485	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798486	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798487	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798488	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798489	0.85[EUR][1000 genomes]
rs798490	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798491	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798492	0.82[ASN][1000 genomes]
rs798493	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798494	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798495	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798496	0.81[EUR][1000 genomes]
rs798497	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs798498	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798499	0.82[ASN][1000 genomes]
rs798500	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs798502	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs798506	0.82[EUR][1000 genomes]
rs798508	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798511	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798512	0.82[ASN][1000 genomes]
rs798513	0.82[ASN][1000 genomes]
rs798514	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798518	0.82[AMR][1000 genomes]
rs798526	0.83[EUR][1000 genomes]
rs798528	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798531	0.82[ASN][1000 genomes]
rs960273	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	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
7	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2644294	GNA12	cis	Nerve Tibial	GTEx
rs2644294	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2644294	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:114 , 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	chr7:2801000-2827600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:2801000-2829600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:2801000-2831600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:2801000-2831600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:2802600-2826400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:2803400-2833400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:2803600-2824200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:2803600-2826800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:2803800-2823800	Weak transcription	NH-A	brain
16	chr7:2803800-2824200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:2807800-2827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
20	chr7:2811400-2824800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:2811600-2824200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:2812600-2831400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr7:2813800-2825200	Weak transcription	HSMM	muscle
24	chr7:2813800-2829200	Weak transcription	Esophagus	oesophagus
25	chr7:2814200-2823800	Weak transcription	Lung	lung
26	chr7:2814400-2838800	Weak transcription	K562	blood
27	chr7:2814600-2824200	Weak transcription	Fetal Kidney	kidney
28	chr7:2815000-2825800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:2815600-2829200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:2815600-2831600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:2815800-2824200	Weak transcription	Brain Hippocampus Middle	brain
32	chr7:2815800-2824400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
34	chr7:2816000-2824200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr7:2816200-2828000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:2816200-2831600	Weak transcription	Brain Angular Gyrus	brain
37	chr7:2816400-2825600	Weak transcription	Gastric	stomach
38	chr7:2816400-2825800	Weak transcription	Fetal Brain Female	brain
39	chr7:2816400-2826400	Weak transcription	Spleen	Spleen
40	chr7:2816400-2831600	Weak transcription	Brain Substantia Nigra	brain
41	chr7:2816600-2824800	Weak transcription	Fetal Lung	lung
42	chr7:2816600-2825800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr7:2816600-2826400	Weak transcription	Liver	Liver
44	chr7:2816800-2825600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:2816800-2826200	Weak transcription	Primary T cells from cord blood	blood
46	chr7:2816800-2826200	Weak transcription	Fetal Intestine Large	intestine
47	chr7:2817000-2825600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:2817000-2829400	Weak transcription	Colonic Mucosa	Colon
49	chr7:2817400-2824400	Weak transcription	NHEK	skin
50	chr7:2817400-2825200	Weak transcription	Dnd41	blood

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