Variant report

Variant	rs1713920
Chromosome Location	chr7:2880935-2880936
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2857161..2858928-chr7:2879727..2881596,2	MCF-7	breast:
2	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:
3	chr7:2726313..2732670-chr7:2878755..2886203,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231357	Chromatin interaction
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1182172	1.00[ASN][1000 genomes]
rs1182173	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1182174	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1182175	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1182176	0.92[ASN][1000 genomes]
rs1182177	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1182178	0.95[ASN][1000 genomes]
rs1182179	0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1182180	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182181	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1182182	0.91[ASN][1000 genomes]
rs1182183	0.91[ASN][1000 genomes]
rs1182184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1182185	0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1182186	0.90[ASN][1000 genomes]
rs1182187	0.94[ASN][1000 genomes]
rs1182188	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1182189	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1182190	0.83[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1182191	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182192	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182193	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182194	0.85[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1182195	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182196	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1182209	0.84[CEU][hapmap]
rs1183085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1636264	0.82[CHB][hapmap]
rs2248390	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2251491	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2266922	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs2283779	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs2283783	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2283784	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2527683	0.82[AMR][1000 genomes]
rs2527684	0.84[CEU][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes]
rs2527686	0.95[YRI][hapmap]
rs2527687	0.88[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2527690	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2527692	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2527694	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2527695	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2527696	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2533878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2644274	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644275	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644295	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644296	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644297	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2644298	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2644304	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6970963	0.81[AMR][1000 genomes]
rs6978692	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs757791	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7777484	0.89[CEU][hapmap];0.80[YRI][hapmap]
rs7807978	0.84[CEU][hapmap]
rs798485	0.83[JPT][hapmap]
rs798486	0.83[JPT][hapmap]
rs798490	0.83[JPT][hapmap]
rs798497	0.83[JPT][hapmap]
rs798499	0.85[CEU][hapmap]
rs798500	0.83[JPT][hapmap]
rs798503	0.81[CEU][hapmap]
rs798512	0.81[CEU][hapmap]
rs798548	0.91[JPT][hapmap]
rs798554	0.91[JPT][hapmap]
rs798556	0.91[JPT][hapmap]
rs798557	0.93[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	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
9	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1713920	GNA12	cis	multi-tissue	Pritchard
rs1713920	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs1713920	GNA12	cis	Artery Tibial	GTEx
rs1713920		cis	Lymphoblastoid	GTEx
rs1713920	LOC392620	cis	multi-tissue	Pritchard
rs1713920	GNA12	cis	Nerve Tibial	GTEx

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	chr7:2861000-2881800	Weak transcription	Colonic Mucosa	Colon
3	chr7:2861400-2882200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
5	chr7:2861800-2882400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:2862800-2882400	Weak transcription	A549	lung
8	chr7:2863800-2881600	Weak transcription	HMEC	breast
9	chr7:2864200-2881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
11	chr7:2864800-2881800	Weak transcription	Fetal Thymus	thymus
12	chr7:2865000-2882400	Weak transcription	Fetal Kidney	kidney
13	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
14	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:2870400-2881400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:2872400-2881200	Weak transcription	Pancreas	Pancrea
17	chr7:2872600-2882800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:2872800-2881000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:2872800-2882600	Weak transcription	Psoas Muscle	Psoas
20	chr7:2872800-2882800	Weak transcription	Liver	Liver
21	chr7:2874600-2881200	Weak transcription	Right Ventricle	heart
22	chr7:2874600-2882400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:2874800-2882000	Weak transcription	NH-A	brain
24	chr7:2874800-2882800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:2875000-2882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:2875200-2881000	Weak transcription	Brain Anterior Caudate	brain
27	chr7:2875400-2881200	Weak transcription	Fetal Brain Female	brain
28	chr7:2875400-2882000	Weak transcription	Gastric	stomach
29	chr7:2875600-2881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:2876000-2881800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:2876000-2882400	Weak transcription	HSMM	muscle
32	chr7:2876200-2881000	Weak transcription	Brain Germinal Matrix	brain
33	chr7:2876200-2882000	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:2876200-2882000	Weak transcription	Ovary	ovary
35	chr7:2876200-2882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:2876400-2881600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:2876400-2881800	Enhancers	Primary B cells from peripheral blood	blood
38	chr7:2876600-2881000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr7:2876800-2881200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:2876800-2882000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:2877000-2881600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:2877000-2882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:2877200-2882200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:2877400-2881000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:2877400-2882000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr7:2877400-2882800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:2877600-2881000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:2877600-2881400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:2877600-2882000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr7:2877600-2882400	Weak transcription	Primary T cells from cord blood	blood

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