Variant report

Variant	rs2251718
Chromosome Location	chr7:2850604-2850605
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2727601..2730936-chr7:2847456..2852448,6	MCF-7	breast:
2	chr7:2850439..2853182-chr7:2881989..2885398,4	MCF-7	breast:
3	chr7:2793932..2796644-chr7:2849190..2850814,2	MCF-7	breast:
4	chr7:2850376..2852421-chr7:2873573..2876256,2	MCF-7	breast:
5	chr7:2850088..2852383-chr7:2882234..2885067,2	MCF-7	breast:
6	chr7:2841478..2843040-chr7:2849710..2851515,2	MCF-7	breast:
7	chr7:2796849..2800870-chr7:2849317..2851659,5	MCF-7	breast:
8	chr7:2843836..2848178-chr7:2849131..2851589,3	MCF-7	breast:
9	chr7:2849209..2851145-chr7:2867571..2870475,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction
ENSG00000231357	Chromatin interaction
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1182206	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2057918	0.90[ASN][1000 genomes]
rs208346	0.84[ASN][1000 genomes]
rs208356	0.83[ASN][1000 genomes]
rs2255541	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255782	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2258960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2266923	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527682	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527689	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644272	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644276	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644311	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846992	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs709280	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709281	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs757789	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757790	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798501	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798504	0.81[EUR][1000 genomes]
rs798509	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798515	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798516	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798517	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798519	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798520	0.80[ASN][1000 genomes]
rs798521	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798522	0.80[ASN][1000 genomes]
rs798523	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798524	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798525	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798527	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs798529	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798530	0.80[EUR][1000 genomes];0.80[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2251718	GNA12	cis	Artery Tibial	GTEx
rs2251718	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2839400-2850800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:2842400-2850800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:2842600-2869400	Weak transcription	Primary T cells from cord blood	blood
4	chr7:2842800-2850800	Weak transcription	HMEC	breast
5	chr7:2842800-2851800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:2843000-2860800	Weak transcription	Esophagus	oesophagus
7	chr7:2843200-2850800	Weak transcription	Aorta	Aorta
8	chr7:2843200-2855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:2843200-2857400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
11	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:2843400-2854400	Weak transcription	Colonic Mucosa	Colon
13	chr7:2843600-2852800	Weak transcription	Dnd41	blood
14	chr7:2843600-2857200	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:2843600-2860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:2843800-2854800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:2844000-2858800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:2844200-2853400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:2845000-2853000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:2845800-2862200	Weak transcription	K562	blood
22	chr7:2847400-2853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:2847800-2858800	Weak transcription	HSMM	muscle
24	chr7:2848000-2850800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:2848000-2851800	Weak transcription	Fetal Kidney	kidney
26	chr7:2848200-2850800	Weak transcription	Fetal Lung	lung
27	chr7:2848200-2851000	Weak transcription	Fetal Thymus	thymus
28	chr7:2848200-2851400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:2848200-2852000	Enhancers	Hela-S3	cervix
30	chr7:2848200-2858800	Weak transcription	NHEK	skin
31	chr7:2848400-2850800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:2848400-2850800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:2848400-2853600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:2848400-2853600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:2848400-2858800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:2848400-2859400	Weak transcription	Fetal Intestine Large	intestine
37	chr7:2848600-2850800	Weak transcription	Fetal Heart	heart
38	chr7:2848600-2851000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:2848600-2852400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr7:2848600-2852600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr7:2848600-2853000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:2848600-2853200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:2848600-2854000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr7:2848600-2854000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:2848800-2850800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:2848800-2850800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:2848800-2851200	Enhancers	NHLF	lung
49	chr7:2848800-2853000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:2848800-2853200	Weak transcription	GM12878-XiMat	blood

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