Variant report

Variant	rs798494
Chromosome Location	chr7:2798294-2798295
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2791509..2794960-chr7:2795693..2799845,4	MCF-7	breast:
2	chr7:2788053..2792290-chr7:2793052..2798708,8	K562	blood:
3	chr7:2777447..2779018-chr7:2797725..2799517,2	K562	blood:
4	chr7:2795602..2798449-chr7:2895895..2897670,2	MCF-7	breast:
5	chr7:2790104..2792525-chr7:2796033..2798907,2	K562	blood:
6	chr7:2766265..2768017-chr7:2797659..2799254,2	K562	blood:
7	chr7:2796622..2799533-chr7:2800643..2803648,3	K562	blood:
8	chr7:2773516..2775458-chr7:2797228..2798920,2	MCF-7	breast:
9	chr7:2796001..2798506-chr7:2858838..2860975,2	MCF-7	breast:
10	chr7:2755108..2759929-chr7:2796424..2799629,5	K562	blood:
11	chr7:2726208..2729496-chr7:2795829..2800431,6	MCF-7	breast:
12	chr7:2725821..2728860-chr7:2795958..2798636,3	MCF-7	breast:
13	chr7:2796509..2799619-chr7:2800643..2805239,7	K562	blood:
14	chr7:2755108..2758694-chr7:2796336..2799311,5	K562	blood:
15	chr7:2796044..2799256-chr7:2882341..2885825,4	K562	blood:
16	chr7:2793193..2795230-chr7:2796231..2799768,5	K562	blood:
17	chr7:2797400..2800902-chr7:2803018..2805102,3	MCF-7	breast:
18	chr7:2795660..2798637-chr7:2882064..2885301,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1182172	0.83[EUR][1000 genomes]
rs1182174	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182176	0.85[EUR][1000 genomes]
rs1182177	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182178	0.85[EUR][1000 genomes]
rs1182179	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182181	0.95[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs1182182	0.84[EUR][1000 genomes]
rs1182183	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182184	0.83[EUR][1000 genomes]
rs1182185	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182186	0.85[EUR][1000 genomes]
rs1182187	0.87[EUR][1000 genomes]
rs1182188	0.95[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1182189	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs1182196	0.93[JPT][hapmap]
rs1182198	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1182207	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1182208	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182209	0.85[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1183085	0.85[EUR][1000 genomes]
rs13243214	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1636264	0.91[CEU][hapmap];0.92[JPT][hapmap]
rs1713919	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2107964	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs2158694	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs2260230	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2266922	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2283779	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2527683	0.86[ASN][1000 genomes]
rs2527684	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2527687	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2533878	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2533879	0.87[EUR][1000 genomes]
rs2533882	0.87[EUR][1000 genomes]
rs2533884	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2644274	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs2644275	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2644294	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644295	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2644296	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs2644297	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs2644312	0.95[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs35957220	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6970963	0.83[ASN][1000 genomes]
rs709282	0.94[ASN][1000 genomes]
rs757791	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs7777484	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs7807978	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs798480	0.94[ASN][1000 genomes]
rs798482	0.94[ASN][1000 genomes]
rs798485	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798486	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798487	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798488	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798489	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs798490	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798492	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs798493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798498	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798499	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs798500	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798502	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798506	0.90[EUR][1000 genomes]
rs798508	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798511	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798512	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs798513	0.94[ASN][1000 genomes]
rs798514	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798518	0.87[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798526	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798528	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798531	0.94[ASN][1000 genomes]
rs798536	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798540	0.86[ASN][1000 genomes]
rs798544	0.83[ASN][1000 genomes]
rs798545	0.83[ASN][1000 genomes]
rs798546	0.83[ASN][1000 genomes]
rs798547	0.87[ASN][1000 genomes]
rs798548	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs798550	0.87[ASN][1000 genomes]
rs798551	0.87[ASN][1000 genomes]
rs798552	0.87[ASN][1000 genomes]
rs798554	0.82[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798555	0.91[ASN][1000 genomes]
rs798556	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798557	0.84[CHB][hapmap];0.91[ASN][1000 genomes]
rs798558	0.87[ASN][1000 genomes]
rs798559	0.88[ASN][1000 genomes]
rs798560	0.88[ASN][1000 genomes]
rs798562	0.90[ASN][1000 genomes]
rs798565	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs960273	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs798494	GNA12	cis	Nerve Tibial	GTEx
rs798494		cis	Lymphoblastoid	GTEx
rs798494	LOC392620	cis	multi-tissue	Pritchard
rs798494	GNA12	cis	Artery Tibial	GTEx
rs798494	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798494	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
4	chr7:2790400-2799800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:2791200-2803400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:2791400-2800200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:2792200-2799400	Weak transcription	Gastric	stomach
8	chr7:2793400-2799200	Weak transcription	Fetal Brain Male	brain
9	chr7:2794800-2799000	Weak transcription	Fetal Brain Female	brain
10	chr7:2795400-2799400	Weak transcription	Liver	Liver
11	chr7:2796400-2798400	Enhancers	Esophagus	oesophagus
12	chr7:2796400-2798600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:2796400-2798800	Enhancers	Ovary	ovary
14	chr7:2796400-2798800	Enhancers	Right Atrium	heart
15	chr7:2796400-2800600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr7:2796400-2801000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr7:2796400-2801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:2796400-2803200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr7:2796400-2804000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr7:2796600-2799800	Enhancers	Fetal Muscle Trunk	muscle
21	chr7:2796800-2798800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:2796800-2799600	Enhancers	Fetal Stomach	stomach
23	chr7:2796800-2799800	Enhancers	Fetal Heart	heart
24	chr7:2796800-2801000	Enhancers	Fetal Intestine Large	intestine
25	chr7:2796800-2802000	Enhancers	Adipose Nuclei	Adipose
26	chr7:2796800-2803600	Weak transcription	Primary B cells from cord blood	blood
27	chr7:2796800-2804400	Enhancers	Fetal Muscle Leg	muscle
28	chr7:2797000-2798400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr7:2797000-2798400	Genic enhancers	Fetal Intestine Small	intestine
30	chr7:2797000-2798400	Enhancers	Pancreas	Pancrea
31	chr7:2797000-2798400	Flanking Active TSS	Hela-S3	cervix
32	chr7:2797000-2798600	Enhancers	Stomach Mucosa	stomach
33	chr7:2797000-2798800	Enhancers	Left Ventricle	heart
34	chr7:2797000-2799200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:2797000-2799200	Enhancers	Spleen	Spleen
36	chr7:2797000-2799400	Enhancers	Duodenum Mucosa	Duodenum
37	chr7:2797000-2799800	Enhancers	Brain Angular Gyrus	brain
38	chr7:2797000-2799800	Enhancers	Brain Substantia Nigra	brain
39	chr7:2797000-2800200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr7:2797000-2800800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr7:2797000-2800800	Enhancers	Primary hematopoietic stem cells	blood
42	chr7:2797000-2801000	Enhancers	Brain Germinal Matrix	brain
43	chr7:2797000-2801000	Enhancers	Fetal Thymus	thymus
44	chr7:2797000-2801800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:2797000-2803200	Enhancers	Right Ventricle	heart
46	chr7:2797000-2803800	Enhancers	Brain Cingulate Gyrus	brain
47	chr7:2797000-2805400	Enhancers	Placenta	Placenta
48	chr7:2797200-2798600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr7:2797200-2799600	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr7:2797200-2801000	Enhancers	Small Intestine	intestine

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