Variant report

Variant	rs798503
Chromosome Location	chr7:2789704-2789705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2788053..2792290-chr7:2793052..2798708,8	K562	blood:
2	chr7:2777523..2779993-chr7:2788582..2791308,2	MCF-7	breast:
3	chr7:2788942..2791836-chr7:2793364..2795418,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1182175	0.88[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap]
rs1182180	0.80[AFR][1000 genomes]
rs1182190	1.00[ASW][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1182191	0.80[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1182192	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1182193	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1182194	0.81[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1182196	0.81[CEU][hapmap]
rs1182209	0.92[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1636264	0.82[ASW][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap]
rs1713920	0.81[CEU][hapmap]
rs2248390	0.83[AFR][1000 genomes]
rs2251491	0.81[AFR][1000 genomes]
rs2266922	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2283779	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2283784	0.81[AFR][1000 genomes]
rs2527683	0.82[EUR][1000 genomes]
rs2527684	0.88[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2527687	0.84[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs2527690	0.82[CEU][hapmap];0.90[YRI][hapmap]
rs2527695	0.84[AFR][1000 genomes]
rs2527696	0.83[AFR][1000 genomes]
rs2533885	0.82[AFR][1000 genomes]
rs2644274	0.83[CEU][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap]
rs2644275	0.84[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs2644295	0.84[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs2644296	0.83[ASW][hapmap];0.84[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.88[YRI][hapmap]
rs2644297	0.87[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2644306	0.92[YRI][hapmap]
rs6970963	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6978692	0.84[AFR][1000 genomes]
rs709282	0.85[EUR][1000 genomes]
rs757786	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs757791	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs7777484	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7807978	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798480	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs798481	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs798482	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs798492	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798498	0.81[CHB][hapmap]
rs798499	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798500	0.81[CHB][hapmap]
rs798502	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs798506	0.96[ASN][1000 genomes]
rs798512	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798513	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs798518	0.81[CHB][hapmap]
rs798528	0.81[CHB][hapmap]
rs798531	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv966746	chr7:2781545-2797621	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1032282	chr7:2789555-2820774	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs798503	LOC392620	cis	multi-tissue	Pritchard
rs798503		cis	Lymphoblastoid	GTEx
rs798503	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798503	NUDT1	cis	parietal	SCAN
rs798503	GNA12	cis	lymphoblastoid	seeQTL
rs798503	GNA12	cis	Nerve Tibial	GTEx
rs798503	GNA12	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:2761000-2796200	Weak transcription	Hela-S3	cervix
3	chr7:2761000-2797000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:2771200-2796200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:2771400-2796200	Weak transcription	NHEK	skin
6	chr7:2773200-2796200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:2773200-2796400	Weak transcription	NH-A	brain
8	chr7:2773200-2797000	Weak transcription	Pancreas	Pancrea
9	chr7:2773600-2796400	Weak transcription	Osteobl	bone
10	chr7:2775200-2790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:2775200-2791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:2775200-2796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:2775400-2789800	Weak transcription	Ovary	ovary
14	chr7:2775400-2790000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:2775400-2797400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
17	chr7:2775800-2796400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:2775800-2796400	Weak transcription	HSMM	muscle
19	chr7:2776200-2797000	Weak transcription	Spleen	Spleen
20	chr7:2776800-2793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:2776800-2796200	Weak transcription	HepG2	liver
22	chr7:2777600-2796200	Weak transcription	Dnd41	blood
23	chr7:2778200-2796400	Weak transcription	Psoas Muscle	Psoas
24	chr7:2778600-2790800	Weak transcription	Adipose Nuclei	Adipose
25	chr7:2778600-2794800	Weak transcription	Primary B cells from cord blood	blood
26	chr7:2778600-2796200	Weak transcription	Fetal Lung	lung
27	chr7:2778600-2796400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:2778800-2789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:2778800-2795800	Weak transcription	Placenta	Placenta
30	chr7:2778800-2796200	Weak transcription	NHLF	lung
31	chr7:2779000-2796600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:2779400-2790400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:2779600-2796000	Weak transcription	Fetal Intestine Small	intestine
34	chr7:2780200-2789800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:2780200-2796200	Weak transcription	Fetal Stomach	stomach
36	chr7:2781600-2789800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:2782800-2797000	Weak transcription	Right Ventricle	heart
38	chr7:2782800-2797200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:2783000-2795600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:2783000-2798000	Weak transcription	Lung	lung
41	chr7:2783600-2796800	Weak transcription	Fetal Intestine Large	intestine
42	chr7:2783800-2790000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:2783800-2790600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:2783800-2797200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr7:2787400-2796200	Weak transcription	HSMMtube	muscle
46	chr7:2788400-2789800	Weak transcription	Aorta	Aorta
47	chr7:2788400-2797400	Weak transcription	Thymus	Thymus
48	chr7:2789000-2790600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:2789400-2790000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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