Variant report

Variant	rs2533890
Chromosome Location	chr7:2828743-2828744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2258709	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527684	0.89[AFR][1000 genomes]
rs2527686	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533885	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2533886	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533888	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644306	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644307	0.91[ASN][1000 genomes]
rs757786	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs757787	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7790322	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	esv3410362	chr7:2828629-2829199	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	inside rSNPs	diseases
10	esv3478146	chr7:2828694-2829175	Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2533890	GNA12	cis	Artery Tibial	GTEx
rs2533890	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs2533890	GNA12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
3	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:2801000-2829600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:2801000-2831600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:2801000-2831600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:2803400-2833400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:2810600-2842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:2810800-2840800	Weak transcription	Stomach Mucosa	stomach
10	chr7:2812600-2831400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:2813800-2829200	Weak transcription	Esophagus	oesophagus
12	chr7:2814400-2838800	Weak transcription	K562	blood
13	chr7:2815600-2829200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:2815600-2831600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:2815800-2840600	Weak transcription	Fetal Brain Male	brain
16	chr7:2816200-2831600	Weak transcription	Brain Angular Gyrus	brain
17	chr7:2816400-2831600	Weak transcription	Brain Substantia Nigra	brain
18	chr7:2817000-2829400	Weak transcription	Colonic Mucosa	Colon
19	chr7:2818400-2831200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:2819200-2831600	Weak transcription	Hela-S3	cervix
21	chr7:2822400-2835000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:2822600-2841000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:2822800-2829600	Weak transcription	Fetal Thymus	thymus
24	chr7:2822800-2834800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:2823600-2835000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:2824000-2842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:2824400-2836600	Weak transcription	Small Intestine	intestine
28	chr7:2824800-2834800	Strong transcription	Fetal Intestine Small	intestine
29	chr7:2824800-2835000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:2825000-2829000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:2825000-2829200	Weak transcription	Brain Anterior Caudate	brain
32	chr7:2825000-2830600	Weak transcription	HMEC	breast
33	chr7:2825000-2831000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:2825000-2835000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:2825000-2835000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:2825200-2829200	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:2825200-2830000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:2825200-2831200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:2825200-2831200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:2825200-2831600	Weak transcription	Fetal Kidney	kidney
41	chr7:2825200-2834800	Strong transcription	NHLF	lung
42	chr7:2825400-2829600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr7:2825400-2830800	Weak transcription	NH-A	brain
44	chr7:2825400-2831200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:2825400-2831800	Weak transcription	GM12878-XiMat	blood
46	chr7:2825400-2831800	Weak transcription	HUVEC	blood vessel
47	chr7:2825600-2829200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:2825600-2829200	Strong transcription	Placenta	Placenta
49	chr7:2825600-2829400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr7:2825600-2829400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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