Variant report

Variant	rs2527683
Chromosome Location	chr7:2825591-2825592
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2816808..2818862-chr7:2824374..2826830,2	K562	blood:
2	chr7:2820643..2823632-chr7:2824452..2826703,2	K562	blood:
3	chr7:2825414..2827300-chr7:2829208..2831201,2	K562	blood:
4	chr7:2802572..2804295-chr7:2824377..2826517,2	MCF-7	breast:
5	chr7:2815376..2818308-chr7:2821717..2825874,3	K562	blood:
6	chr7:2822854..2825744-chr7:2825933..2828348,2	MCF-7	breast:
7	chr7:2825414..2828285-chr7:2829208..2832535,3	K562	blood:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1182173	0.83[AMR][1000 genomes]
rs1182175	0.83[AMR][1000 genomes]
rs1182180	0.84[AMR][1000 genomes]
rs1182190	0.86[AMR][1000 genomes]
rs1182191	0.86[AMR][1000 genomes]
rs1182192	0.86[AMR][1000 genomes]
rs1182193	0.86[AMR][1000 genomes]
rs1182194	0.86[AMR][1000 genomes]
rs1182195	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1182196	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1182198	0.86[ASN][1000 genomes]
rs1182199	0.85[ASN][1000 genomes]
rs1182207	0.89[ASN][1000 genomes]
rs1182208	0.94[ASN][1000 genomes]
rs1182209	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13243214	0.96[ASN][1000 genomes]
rs1713919	0.81[ASN][1000 genomes]
rs1713920	0.82[AMR][1000 genomes]
rs2107964	0.84[ASN][1000 genomes]
rs2158694	0.83[ASN][1000 genomes]
rs2248390	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2251491	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2260230	1.00[ASN][1000 genomes]
rs2266922	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283779	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283783	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283784	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527684	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527687	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2527690	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2527692	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527694	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527695	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2527696	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2533879	0.87[ASN][1000 genomes]
rs2533882	0.89[ASN][1000 genomes]
rs2644274	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2644275	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2644294	1.00[ASN][1000 genomes]
rs2644295	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644296	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2644297	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2644298	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2644304	0.80[AMR][1000 genomes]
rs2644312	0.91[ASN][1000 genomes]
rs35957220	0.95[ASN][1000 genomes]
rs6970963	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6978692	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs709282	0.82[ASN][1000 genomes]
rs757791	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7777484	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7807978	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798480	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798481	0.83[EUR][1000 genomes]
rs798482	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798485	0.91[ASN][1000 genomes]
rs798486	0.91[ASN][1000 genomes]
rs798487	0.91[ASN][1000 genomes]
rs798488	0.90[ASN][1000 genomes]
rs798490	0.90[ASN][1000 genomes]
rs798491	0.86[ASN][1000 genomes]
rs798492	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798493	0.86[ASN][1000 genomes]
rs798494	0.86[ASN][1000 genomes]
rs798495	0.86[ASN][1000 genomes]
rs798497	0.87[ASN][1000 genomes]
rs798498	0.84[ASN][1000 genomes]
rs798499	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798500	0.87[ASN][1000 genomes]
rs798503	0.82[EUR][1000 genomes]
rs798508	0.85[ASN][1000 genomes]
rs798511	0.85[ASN][1000 genomes]
rs798512	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798513	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798514	0.85[ASN][1000 genomes]
rs798528	0.83[ASN][1000 genomes]
rs798531	0.82[ASN][1000 genomes]
rs960273	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2527683	GNA12	cis	Nerve Tibial	GTEx
rs2527683	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr7:2803600-2826800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:2807800-2827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
17	chr7:2812600-2831400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr7:2813800-2829200	Weak transcription	Esophagus	oesophagus
19	chr7:2814400-2838800	Weak transcription	K562	blood
20	chr7:2815000-2825800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:2815600-2829200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:2815600-2831600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
24	chr7:2816200-2828000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:2816200-2831600	Weak transcription	Brain Angular Gyrus	brain
26	chr7:2816400-2825600	Weak transcription	Gastric	stomach
27	chr7:2816400-2825800	Weak transcription	Fetal Brain Female	brain
28	chr7:2816400-2826400	Weak transcription	Spleen	Spleen
29	chr7:2816400-2831600	Weak transcription	Brain Substantia Nigra	brain
30	chr7:2816600-2825800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr7:2816600-2826400	Weak transcription	Liver	Liver
32	chr7:2816800-2825600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:2816800-2826200	Weak transcription	Primary T cells from cord blood	blood
34	chr7:2816800-2826200	Weak transcription	Fetal Intestine Large	intestine
35	chr7:2817000-2825600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:2817000-2829400	Weak transcription	Colonic Mucosa	Colon
37	chr7:2817400-2825800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:2817800-2826400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:2818000-2827400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:2818400-2831200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:2818800-2825800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr7:2819000-2826400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:2819200-2831600	Weak transcription	Hela-S3	cervix
44	chr7:2819600-2825600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:2819600-2825600	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:2820400-2826400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr7:2820800-2825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:2821600-2827000	Weak transcription	Psoas Muscle	Psoas
49	chr7:2821800-2826000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:2822200-2825600	Weak transcription	Primary hematopoietic stem cells	blood

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