Variant report

Variant	rs1182173
Chromosome Location	chr7:2878016-2878017
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57922933..57924665-chr7:2875857..2878835,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1182172	0.95[ASN][1000 genomes]
rs1182174	0.96[ASN][1000 genomes]
rs1182175	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1182176	0.96[ASN][1000 genomes]
rs1182177	0.92[ASN][1000 genomes]
rs1182178	0.91[ASN][1000 genomes]
rs1182179	0.95[ASN][1000 genomes]
rs1182180	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182181	0.91[ASN][1000 genomes]
rs1182182	0.95[ASN][1000 genomes]
rs1182183	0.95[ASN][1000 genomes]
rs1182184	0.91[ASN][1000 genomes]
rs1182185	0.95[ASN][1000 genomes]
rs1182186	0.94[ASN][1000 genomes]
rs1182187	0.90[ASN][1000 genomes]
rs1182188	0.88[ASN][1000 genomes]
rs1182189	0.88[ASN][1000 genomes]
rs1182190	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182191	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1182192	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1182193	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1182194	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182195	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1182196	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182209	0.80[AMR][1000 genomes]
rs1183085	0.93[ASN][1000 genomes]
rs1713920	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248390	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2251491	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2266922	0.88[AMR][1000 genomes]
rs2283783	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2283784	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2527683	0.83[AMR][1000 genomes]
rs2527684	0.87[AMR][1000 genomes]
rs2527687	0.82[AMR][1000 genomes]
rs2527690	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2527692	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2527694	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2527695	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2527696	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2533878	0.95[ASN][1000 genomes]
rs2644274	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2644275	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2644295	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644296	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644297	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2644298	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644304	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970963	0.88[AMR][1000 genomes]
rs6978692	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs757791	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798492	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	nsv1019463	chr7:2848448-2881872	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1182173	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1182173	GNA12	cis	Nerve Tibial	GTEx
rs1182173	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
2	chr7:2861000-2881800	Weak transcription	Colonic Mucosa	Colon
3	chr7:2861400-2882200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
5	chr7:2861800-2882400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:2862800-2882400	Weak transcription	A549	lung
8	chr7:2863000-2878600	Weak transcription	Small Intestine	intestine
9	chr7:2863800-2881600	Weak transcription	HMEC	breast
10	chr7:2864200-2881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
12	chr7:2864800-2878600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:2864800-2881800	Weak transcription	Fetal Thymus	thymus
14	chr7:2865000-2882400	Weak transcription	Fetal Kidney	kidney
15	chr7:2865200-2878600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:2865400-2878600	Weak transcription	Brain Substantia Nigra	brain
17	chr7:2865400-2879600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
19	chr7:2865600-2880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr7:2870400-2881400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:2871000-2878600	Weak transcription	Hela-S3	cervix
23	chr7:2872200-2878600	Weak transcription	Brain Angular Gyrus	brain
24	chr7:2872400-2881200	Weak transcription	Pancreas	Pancrea
25	chr7:2872600-2882800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:2872800-2880200	Weak transcription	Fetal Intestine Large	intestine
27	chr7:2872800-2881000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:2872800-2882600	Weak transcription	Psoas Muscle	Psoas
29	chr7:2872800-2882800	Weak transcription	Liver	Liver
30	chr7:2873400-2878600	Weak transcription	K562	blood
31	chr7:2874600-2881200	Weak transcription	Right Ventricle	heart
32	chr7:2874600-2882400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:2874800-2882000	Weak transcription	NH-A	brain
34	chr7:2874800-2882800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:2875000-2880000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:2875000-2882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:2875200-2878400	Weak transcription	NHDF-Ad	bronchial
38	chr7:2875200-2881000	Weak transcription	Brain Anterior Caudate	brain
39	chr7:2875400-2878600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr7:2875400-2879000	Weak transcription	Lung	lung
41	chr7:2875400-2880800	Weak transcription	Placenta	Placenta
42	chr7:2875400-2881200	Weak transcription	Fetal Brain Female	brain
43	chr7:2875400-2882000	Weak transcription	Gastric	stomach
44	chr7:2875600-2879600	Weak transcription	NHEK	skin
45	chr7:2875600-2881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:2875800-2879000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:2876000-2880400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:2876000-2881800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:2876000-2882400	Weak transcription	HSMM	muscle
50	chr7:2876200-2878800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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