Variant report

Variant	rs798556
Chromosome Location	chr7:2759002-2759003
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2756196..2760316-chr7:2775723..2779597,5	K562	blood:
2	chr7:2751778..2761552-chr7:2768388..2775125,13	K562	blood:
3	chr7:2757306..2759067-chr7:2759260..2762192,2	K562	blood:
4	chr7:2757202..2759716-chr7:2762662..2764833,2	K562	blood:
5	chr7:2727234..2729043-chr7:2757444..2760192,2	MCF-7	breast:
6	chr7:2724386..2733394-chr7:2753206..2761980,25	MCF-7	breast:
7	chr10:112773361..112773861-chr7:2758450..2759306,2	MCF-7	breast:
8	chr7:2758294..2760218-chr7:2772871..2774400,2	MCF-7	breast:
9	chr7:2758129..2761976-chr7:2763173..2766287,3	MCF-7	breast:
10	chr7:2758388..2761774-chr7:2912256..2915270,3	K562	blood:
11	chr7:2393560..2395423-chr7:2757362..2759137,2	K562	blood:
12	chr7:2710494..2711221-chr7:2758292..2759192,2	MCF-7	breast:
13	chr7:2758216..2760821-chr7:2762447..2764162,2	K562	blood:
14	chr7:2755108..2759929-chr7:2796424..2799629,5	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNA12-2	chr7:2757467-2760269	XLOC_006335

No data

Variant related genes	Relation type
ENSG00000106263	Chromatin interaction
ENSG00000174945	Chromatin interaction
ENSG00000106266	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1182174	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1182175	1.00[JPT][hapmap]
rs1182177	0.92[JPT][hapmap]
rs1182179	1.00[JPT][hapmap]
rs1182181	0.92[JPT][hapmap]
rs1182183	0.82[CEU][hapmap]
rs1182184	0.91[JPT][hapmap]
rs1182185	1.00[JPT][hapmap]
rs1182188	0.92[JPT][hapmap]
rs1182189	0.92[JPT][hapmap]
rs1182190	1.00[JPT][hapmap]
rs1182191	0.92[JPT][hapmap]
rs1182194	1.00[JPT][hapmap]
rs1182207	0.81[ASN][1000 genomes]
rs1182208	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1182209	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1183085	0.92[JPT][hapmap]
rs1713920	0.91[JPT][hapmap]
rs2260230	0.87[CEU][hapmap]
rs2266922	0.91[JPT][hapmap]
rs2283779	0.83[CHB][hapmap]
rs2533878	0.92[JPT][hapmap]
rs2644275	0.86[JPT][hapmap]
rs2644295	0.86[JPT][hapmap]
rs2644296	0.86[JPT][hapmap]
rs709282	0.89[ASN][1000 genomes]
rs757791	0.86[JPT][hapmap]
rs7777484	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs7807978	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs798480	0.83[ASN][1000 genomes]
rs798482	0.83[ASN][1000 genomes]
rs798485	0.86[CEU][hapmap];0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs798486	0.86[CEU][hapmap];0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs798487	0.83[ASN][1000 genomes]
rs798488	0.86[CEU][hapmap];0.82[ASN][1000 genomes]
rs798490	0.86[CEU][hapmap];0.82[ASN][1000 genomes]
rs798491	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798492	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs798493	0.87[ASN][1000 genomes]
rs798494	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798495	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs798496	0.83[ASN][1000 genomes]
rs798497	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798498	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs798499	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs798500	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs798502	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs798508	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798511	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798512	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs798513	0.93[ASN][1000 genomes]
rs798514	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798518	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs798526	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798528	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798531	0.89[ASN][1000 genomes]
rs798536	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798540	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798544	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798545	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798547	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798548	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798550	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798551	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798555	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798557	0.94[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798563	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798565	0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471227	chr7:2629020-2768864	Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv887309	chr7:2664214-2763102	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv887312	chr7:2707822-2763102	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv1017611	chr7:2750418-2781716	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv538654	chr7:2750418-2781716	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	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
11	nsv971480	chr7:2755767-2765866	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv10922	chr7:2757395-2759983	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs798556	GNA12	cis	multi-tissue	Pritchard
rs798556	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798556		cis	Lymphoblastoid	GTEx
rs798556	GNA12	cis	Nerve Tibial	GTEx
rs798556	GNA12	cis	Artery Tibial	GTEx
rs798556	LOC392620	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2742200-2765600	Weak transcription	HSMM	muscle
2	chr7:2749000-2760800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr7:2749400-2770600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:2749800-2759800	Weak transcription	HMEC	breast
5	chr7:2749800-2770800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:2750000-2760400	Weak transcription	Hela-S3	cervix
7	chr7:2750000-2760800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:2750000-2762800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:2750000-2765600	Weak transcription	Brain Substantia Nigra	brain
10	chr7:2750000-2767800	Weak transcription	Osteobl	bone
11	chr7:2750000-2768400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:2750000-2769000	Weak transcription	NHDF-Ad	bronchial
13	chr7:2750200-2765800	Weak transcription	Liver	Liver
14	chr7:2751000-2764400	Weak transcription	Brain Germinal Matrix	brain
15	chr7:2751200-2768400	Weak transcription	Brain Angular Gyrus	brain
16	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:2753400-2760400	Weak transcription	Aorta	Aorta
18	chr7:2753400-2765800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:2753600-2759200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:2753600-2768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:2753800-2760400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:2754000-2759400	Enhancers	Primary B cells from cord blood	blood
23	chr7:2754200-2759400	Enhancers	Primary B cells from peripheral blood	blood
24	chr7:2754400-2759200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr7:2754400-2759200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:2754600-2759200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:2754600-2766800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:2754800-2760600	Enhancers	Primary hematopoietic stem cells	blood
29	chr7:2754800-2774200	Weak transcription	Fetal Brain Male	brain
30	chr7:2755600-2759200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr7:2755800-2761400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:2755800-2770600	Weak transcription	Fetal Kidney	kidney
33	chr7:2756000-2760400	Weak transcription	NH-A	brain
34	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
35	chr7:2756200-2759200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr7:2756200-2759200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:2756200-2759800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:2756200-2761200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr7:2756200-2762800	Weak transcription	HSMMtube	muscle
40	chr7:2756200-2770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr7:2756400-2759200	Bivalent Enhancer	Fetal Thymus	thymus
42	chr7:2756400-2765600	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:2757200-2767400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:2757200-2770600	Weak transcription	Esophagus	oesophagus
45	chr7:2757400-2766200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:2757600-2772800	Weak transcription	Small Intestine	intestine
47	chr7:2757800-2759400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:2757800-2759600	Weak transcription	Gastric	stomach
49	chr7:2757800-2760000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:2757800-2760400	Weak transcription	GM12878-XiMat	blood

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