Variant report

Variant	rs1713921
Chromosome Location	chr7:2882262-2882263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:
2	chr7:2801788..2804432-chr7:2882018..2884117,3	K562	blood:
3	chr7:2726313..2732670-chr7:2878755..2886203,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction
ENSG00000174945	Chromatin interaction
ENSG00000231357	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1182156	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11973498	0.92[ASN][1000 genomes]
rs12700373	0.91[ASN][1000 genomes]
rs13230995	0.92[ASN][1000 genomes]
rs1614791	0.90[ASN][1000 genomes]
rs1623138	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1636247	0.95[ASN][1000 genomes]
rs1636248	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636249	0.93[ASN][1000 genomes]
rs1636250	0.93[ASN][1000 genomes]
rs1636251	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1636252	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636253	0.92[ASN][1000 genomes]
rs1636254	0.92[ASN][1000 genomes]
rs1636255	0.90[ASN][1000 genomes]
rs1636256	0.81[ASN][1000 genomes]
rs1639034	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1639036	0.93[ASN][1000 genomes]
rs1639040	0.93[ASN][1000 genomes]
rs1639064	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1639065	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1639066	0.90[ASN][1000 genomes]
rs1713913	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2527677	0.94[ASN][1000 genomes]
rs2527680	0.90[ASN][1000 genomes]
rs2527681	0.89[ASN][1000 genomes]
rs2533867	0.92[ASN][1000 genomes]
rs2533868	0.92[ASN][1000 genomes]
rs2533870	0.92[ASN][1000 genomes]
rs2533871	0.94[ASN][1000 genomes]
rs2533875	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2533877	0.96[ASN][1000 genomes]
rs2533891	0.90[ASN][1000 genomes]
rs2644281	0.92[ASN][1000 genomes]
rs2644286	0.92[ASN][1000 genomes]
rs2644293	0.90[ASN][1000 genomes]
rs2644300	0.94[ASN][1000 genomes]
rs2644309	0.90[ASN][1000 genomes]
rs2679259	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71522301	0.91[ASN][1000 genomes]

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	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
2	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
3	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
4	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
5	nsv887313	chr7:2875420-2927120	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv887314	chr7:2875420-2944187	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1713921	GNA12	cis	Nerve Tibial	GTEx
rs1713921	GNA12	cis	multi-tissue	Pritchard
rs1713921	GNA12	cis	Artery Tibial	GTEx
rs1713921	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
2	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
3	chr7:2861800-2882400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:2862800-2882400	Weak transcription	A549	lung
6	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
7	chr7:2865000-2882400	Weak transcription	Fetal Kidney	kidney
8	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
9	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:2872600-2882800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:2872800-2882600	Weak transcription	Psoas Muscle	Psoas
12	chr7:2872800-2882800	Weak transcription	Liver	Liver
13	chr7:2874600-2882400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:2874800-2882800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:2875000-2882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:2876000-2882400	Weak transcription	HSMM	muscle
17	chr7:2876200-2882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:2877400-2882800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:2877600-2882400	Weak transcription	Primary T cells from cord blood	blood
20	chr7:2877600-2882600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:2877600-2882600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr7:2877800-2882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:2877800-2882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:2878000-2882400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr7:2878000-2882600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr7:2878000-2882800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr7:2878200-2882600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:2878200-2882800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:2878400-2882800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:2879000-2882400	Weak transcription	NHLF	lung
31	chr7:2879000-2882600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:2879000-2882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:2879200-2882800	Weak transcription	Small Intestine	intestine
34	chr7:2879400-2882600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:2879800-2883400	Enhancers	Fetal Heart	heart
36	chr7:2880800-2882400	Enhancers	Colon Smooth Muscle	Colon
37	chr7:2880800-2882400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr7:2880800-2882800	Enhancers	Left Ventricle	heart
39	chr7:2881000-2882400	Enhancers	Right Atrium	heart
40	chr7:2881000-2882400	Enhancers	Hela-S3	cervix
41	chr7:2881000-2882800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr7:2881000-2883000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:2881000-2883000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
44	chr7:2881200-2882400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:2881200-2882400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:2881200-2882400	Enhancers	Brain Angular Gyrus	brain
47	chr7:2881200-2882600	Enhancers	Rectal Smooth Muscle	rectum
48	chr7:2881200-2882800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr7:2881200-2882800	Enhancers	Pancreas	Pancrea
50	chr7:2881200-2882800	Enhancers	Right Ventricle	heart

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