Variant report

Variant	rs2644272
Chromosome Location	chr7:2856443-2856444
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr7:2856372-2856520	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2855867..2858678-chr7:2858785..2861343,3	MCF-7	breast:

Variant related genes	Relation type
GNA12	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1182206	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2057918	0.88[ASN][1000 genomes]
rs208345	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs208346	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs208354	0.90[CHB][hapmap]
rs208356	0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2251718	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255541	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255782	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2258709	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2258960	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2266923	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2266925	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs2527682	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527686	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2527689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533886	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2533888	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2644276	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644306	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2644311	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]
rs3846992	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs709280	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs709281	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs757786	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs757789	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757790	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7790322	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs798501	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798504	0.81[EUR][1000 genomes]
rs798509	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs798515	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798516	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798517	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798519	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798521	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798522	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs798523	0.84[EUR][1000 genomes]
rs798524	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798525	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798527	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs798529	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs798530	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs798532	0.86[CHB][hapmap]
rs798549	0.82[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2644272	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2644272	GNA12	cis	Artery Tibial	GTEx
rs2644272	GNA12	cis	lymphoblastoid	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2842600-2869400	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2843000-2860800	Weak transcription	Esophagus	oesophagus
3	chr7:2843200-2857400	Weak transcription	Brain Germinal Matrix	brain
4	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
5	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:2843600-2857200	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:2843600-2860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr7:2844000-2858800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:2845800-2862200	Weak transcription	K562	blood
11	chr7:2847800-2858800	Weak transcription	HSMM	muscle
12	chr7:2848200-2858800	Weak transcription	NHEK	skin
13	chr7:2848400-2858800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:2848400-2859400	Weak transcription	Fetal Intestine Large	intestine
15	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:2848800-2857200	Weak transcription	Brain Substantia Nigra	brain
17	chr7:2848800-2858400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:2848800-2858600	Weak transcription	Gastric	stomach
19	chr7:2848800-2863400	Weak transcription	Fetal Brain Female	brain
20	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:2849000-2857200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:2849400-2860800	Weak transcription	Stomach Mucosa	stomach
23	chr7:2849600-2866000	Enhancers	Placenta	Placenta
24	chr7:2851000-2857600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:2851000-2860200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:2851200-2857600	Weak transcription	Fetal Heart	heart
27	chr7:2851200-2858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:2851600-2858600	Weak transcription	HMEC	breast
29	chr7:2851600-2858800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:2851600-2860600	Weak transcription	Primary B cells from cord blood	blood
31	chr7:2851600-2861000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:2851600-2861000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr7:2851600-2869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:2851800-2860400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
36	chr7:2852000-2857000	Weak transcription	Liver	Liver
37	chr7:2852000-2857600	Weak transcription	Brain Anterior Caudate	brain
38	chr7:2852000-2858600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:2852000-2858800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:2852000-2860400	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:2852400-2857200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:2852400-2857400	Weak transcription	Fetal Lung	lung
43	chr7:2852600-2857200	Enhancers	Lung	lung
44	chr7:2852600-2857800	Weak transcription	Osteobl	bone
45	chr7:2853200-2857800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:2853200-2860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:2853400-2857200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:2853600-2858400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:2853600-2858800	Weak transcription	Hela-S3	cervix
50	chr7:2853800-2857200	Enhancers	Right Ventricle	heart

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