Variant report

Variant	rs2251491
Chromosome Location	chr7:2852835-2852836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2852392..2854635-chr7:2859767..2862192,2	K562	blood:
2	chr7:2850439..2853182-chr7:2881989..2885398,4	MCF-7	breast:
3	chr7:2851198..2852997-chr7:2868294..2871241,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1182173	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182175	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1182180	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1182190	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182191	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182192	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182193	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182194	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1182195	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1182196	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182197	0.82[AFR][1000 genomes]
rs1182198	0.93[ASN][1000 genomes]
rs1182199	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1182208	0.84[ASN][1000 genomes]
rs1182209	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13243214	0.86[ASN][1000 genomes]
rs1636264	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1713919	0.86[ASN][1000 genomes]
rs1713920	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2107964	0.91[ASN][1000 genomes]
rs2158694	0.90[ASN][1000 genomes]
rs2248390	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2260230	0.88[ASN][1000 genomes]
rs2266922	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283779	0.85[ASN][1000 genomes]
rs2283783	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283784	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527683	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2527684	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2527687	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2527690	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527692	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527694	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527695	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527696	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2533879	0.94[ASN][1000 genomes]
rs2533882	0.94[ASN][1000 genomes]
rs2533885	0.84[AFR][1000 genomes]
rs2644274	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644275	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644294	0.88[ASN][1000 genomes]
rs2644295	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644296	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644297	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644298	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644304	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2644312	0.93[ASN][1000 genomes]
rs35957220	0.85[ASN][1000 genomes]
rs6970963	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6978692	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757786	0.84[AFR][1000 genomes]
rs757791	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7777484	0.89[ASN][1000 genomes]
rs7807978	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798480	0.82[ASN][1000 genomes]
rs798482	0.82[ASN][1000 genomes]
rs798485	0.82[ASN][1000 genomes]
rs798486	0.82[ASN][1000 genomes]
rs798487	0.82[ASN][1000 genomes]
rs798488	0.81[ASN][1000 genomes]
rs798490	0.81[ASN][1000 genomes]
rs798492	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798498	0.82[ASN][1000 genomes]
rs798499	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798503	0.81[AFR][1000 genomes]
rs798512	0.80[ASN][1000 genomes]
rs798513	0.80[ASN][1000 genomes]
rs960273	0.96[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
rs2251491	GNA12	cis	Nerve Tibial	GTEx
rs2251491	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 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	chr7:2843200-2855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:2843200-2857400	Weak transcription	Brain Germinal Matrix	brain
5	chr7:2843200-2860800	Weak transcription	HSMMtube	muscle
6	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr7:2843400-2854400	Weak transcription	Colonic Mucosa	Colon
8	chr7:2843600-2857200	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:2843600-2860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:2843800-2854800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:2844000-2858800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:2844200-2853400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:2845000-2853000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:2845800-2862200	Weak transcription	K562	blood
16	chr7:2847400-2853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:2847800-2858800	Weak transcription	HSMM	muscle
18	chr7:2848200-2858800	Weak transcription	NHEK	skin
19	chr7:2848400-2853600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:2848400-2853600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:2848400-2858800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:2848400-2859400	Weak transcription	Fetal Intestine Large	intestine
23	chr7:2848600-2853000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:2848600-2853200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:2848600-2854000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr7:2848600-2854000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:2848800-2853000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:2848800-2853200	Weak transcription	GM12878-XiMat	blood
30	chr7:2848800-2854400	Weak transcription	Small Intestine	intestine
31	chr7:2848800-2857200	Weak transcription	Brain Substantia Nigra	brain
32	chr7:2848800-2858400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:2848800-2858600	Weak transcription	Gastric	stomach
34	chr7:2848800-2863400	Weak transcription	Fetal Brain Female	brain
35	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:2849000-2853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:2849000-2857200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:2849400-2860800	Weak transcription	Stomach Mucosa	stomach
39	chr7:2849600-2866000	Enhancers	Placenta	Placenta
40	chr7:2849800-2855400	Enhancers	NHDF-Ad	bronchial
41	chr7:2850000-2853200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:2851000-2853000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:2851000-2857600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:2851000-2860200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:2851200-2853000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:2851200-2853000	Weak transcription	Fetal Intestine Small	intestine
47	chr7:2851200-2853000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:2851200-2857600	Weak transcription	Fetal Heart	heart
49	chr7:2851200-2858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:2851600-2853000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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