Variant report

Variant	rs2644311
Chromosome Location	chr7:2845371-2845372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2843836..2848178-chr7:2849131..2851589,3	MCF-7	breast:
2	chr7:2843670..2845376-chr7:2912642..2914150,2	MCF-7	breast:
3	chr7:2838542..2841510-chr7:2843675..2845614,3	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1182206	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2057918	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs208345	0.82[CHB][hapmap]
rs208346	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs208354	0.90[CHB][hapmap]
rs208356	0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs2251718	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255541	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2258709	0.83[CHB][hapmap];0.81[GIH][hapmap]
rs2258960	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2266923	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2266925	0.86[CHB][hapmap]
rs2527682	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527686	0.83[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs2527689	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533886	0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs2533888	0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs2644272	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644306	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs3846992	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709280	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs709281	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757786	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs757789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757790	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790322	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs798501	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798504	0.82[EUR][1000 genomes]
rs798509	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798515	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798516	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798517	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798519	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798521	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798522	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap]
rs798523	0.85[EUR][1000 genomes]
rs798524	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798525	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798527	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798529	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798530	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs798532	0.86[CHB][hapmap]
rs798549	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2644311	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2644311	GNA12	cis	lymphoblastoid	seeQTL
rs2644311	GNA12	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2834600-2847800	Weak transcription	Liver	Liver
2	chr7:2837000-2850600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:2839400-2848600	Enhancers	Fetal Heart	heart
4	chr7:2839400-2850800	Weak transcription	Primary B cells from cord blood	blood
5	chr7:2840400-2846200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr7:2841000-2850200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:2841200-2847400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:2841400-2846400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:2841400-2847000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:2841400-2847400	Weak transcription	GM12878-XiMat	blood
11	chr7:2841400-2847800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:2842200-2845800	Enhancers	Placenta	Placenta
13	chr7:2842400-2845600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:2842400-2845600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:2842400-2845600	Enhancers	Right Ventricle	heart
16	chr7:2842400-2846000	Enhancers	Ovary	ovary
17	chr7:2842400-2850800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:2842600-2845400	Enhancers	Fetal Brain Male	brain
19	chr7:2842600-2850600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:2842600-2869400	Weak transcription	Primary T cells from cord blood	blood
21	chr7:2842800-2845400	Weak transcription	Brain Angular Gyrus	brain
22	chr7:2842800-2847000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:2842800-2850800	Weak transcription	HMEC	breast
24	chr7:2842800-2851800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:2843000-2845400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr7:2843000-2845400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:2843000-2845400	Enhancers	Fetal Intestine Large	intestine
28	chr7:2843000-2845600	Enhancers	Right Atrium	heart
29	chr7:2843000-2847400	Weak transcription	Fetal Brain Female	brain
30	chr7:2843000-2847400	Weak transcription	Pancreas	Pancrea
31	chr7:2843000-2847800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:2843000-2847800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:2843000-2847800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:2843000-2847800	Weak transcription	Spleen	Spleen
35	chr7:2843000-2848200	Weak transcription	Brain Substantia Nigra	brain
36	chr7:2843000-2848600	Weak transcription	Stomach Mucosa	stomach
37	chr7:2843000-2860800	Weak transcription	Esophagus	oesophagus
38	chr7:2843200-2845600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:2843200-2847400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:2843200-2847600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:2843200-2847800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:2843200-2848200	Enhancers	Fetal Lung	lung
43	chr7:2843200-2849800	Weak transcription	Osteobl	bone
44	chr7:2843200-2850200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:2843200-2850600	Weak transcription	Brain Anterior Caudate	brain
46	chr7:2843200-2850800	Weak transcription	Aorta	Aorta
47	chr7:2843200-2855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:2843200-2857400	Weak transcription	Brain Germinal Matrix	brain
49	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
50	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood

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