Variant report

Variant	rs2533886
Chromosome Location	chr7:2834869-2834870
allele	A/G
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	GATA3	chr7:2834400-2835136	SK-N-SH	brain:	n/a	chr7:2834790-2834801
2	NR3C1	chr7:2834409-2834946	A549	lung:	n/a	n/a
3	GATA3	chr7:2834441-2835087	SK-N-SH	brain:	n/a	chr7:2834790-2834801

Variant related genes	Relation type
GNA12	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1182206	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs208346	0.90[JPT][hapmap]
rs208356	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2255541	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2255782	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2258709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2258960	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2266923	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs2527684	0.97[LWK][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs2527686	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527687	0.82[MKK][hapmap]
rs2527689	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2533885	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2533888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533890	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644272	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2644306	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2644307	0.94[ASN][1000 genomes]
rs2644311	0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs3846992	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs709280	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs757786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757787	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7790322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs798515	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs798517	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs798519	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs798521	0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs798522	0.83[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs798525	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs798527	0.83[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs798530	0.83[CHB][hapmap];0.84[JPT][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2533886	GNA12	cis	Artery Tibial	GTEx
rs2533886		cis	Lymphoblastoid	GTEx
rs2533886	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2533886	NUDT1	cis	parietal	SCAN
rs2533886	LOC392620	cis	multi-tissue	Pritchard
rs2533886	GNA12	cis	lymphoblastoid	seeQTL
rs2533886	HEATR2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
3	chr7:2814400-2838800	Weak transcription	K562	blood
4	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
5	chr7:2822400-2835000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:2822600-2841000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:2823600-2835000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:2824000-2842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:2824400-2836600	Weak transcription	Small Intestine	intestine
10	chr7:2824800-2835000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:2825000-2835000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:2825000-2835000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:2825600-2835000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:2825600-2835000	Strong transcription	HepG2	liver
15	chr7:2825600-2835200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:2825600-2835200	Strong transcription	Fetal Muscle Leg	muscle
17	chr7:2826000-2835000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:2826200-2835000	Strong transcription	Fetal Intestine Large	intestine
19	chr7:2826400-2835000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr7:2826400-2835200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:2827200-2835400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:2828000-2836600	Weak transcription	Psoas Muscle	Psoas
23	chr7:2828400-2835000	Strong transcription	Primary B cells from cord blood	blood
24	chr7:2829000-2835000	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr7:2829200-2835000	Strong transcription	Dnd41	blood
26	chr7:2829600-2835000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr7:2829800-2835000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:2829800-2835000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:2829800-2841200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:2829800-2841400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:2830000-2841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:2830200-2842800	Weak transcription	Colonic Mucosa	Colon
33	chr7:2830400-2835200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:2830400-2836200	Weak transcription	Fetal Heart	heart
35	chr7:2830600-2835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:2830600-2835200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:2831000-2835000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:2831200-2835000	Strong transcription	Primary T cells from cord blood	blood
39	chr7:2831200-2835000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr7:2831200-2835000	Strong transcription	NHDF-Ad	bronchial
41	chr7:2831400-2835000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:2831400-2835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:2831400-2835000	Strong transcription	Osteobl	bone
44	chr7:2831600-2835200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:2832000-2841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr7:2832600-2835200	Weak transcription	Thymus	Thymus
47	chr7:2832800-2835600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:2832800-2841000	Weak transcription	NHEK	skin
49	chr7:2832800-2842600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:2833000-2836000	Weak transcription	Aorta	Aorta

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