Variant report

Variant	rs798500
Chromosome Location	chr7:2790685-2790686
allele	A/G
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	chr7:2790103..2793093-chr7:2798943..2803164,4	K562	blood:
4	chr7:2788942..2791836-chr7:2793364..2795418,2	MCF-7	breast:
5	chr7:2790104..2792525-chr7:2796033..2798907,2	K562	blood:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1182172	0.82[EUR][1000 genomes]
rs1182174	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182176	0.84[EUR][1000 genomes]
rs1182177	0.95[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs1182178	0.84[EUR][1000 genomes]
rs1182179	0.95[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1182181	0.95[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1182182	0.84[EUR][1000 genomes]
rs1182183	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1182184	0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs1182185	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs1182186	0.84[EUR][1000 genomes]
rs1182187	0.86[EUR][1000 genomes]
rs1182188	0.95[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1182189	0.87[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1182191	0.84[JPT][hapmap]
rs1182196	0.93[JPT][hapmap]
rs1182197	0.84[CHB][hapmap]
rs1182198	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1182207	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1182208	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182209	0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1183085	0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs13243214	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1636255	0.91[TSI][hapmap]
rs1636264	0.91[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap]
rs1713919	0.95[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1713920	0.83[JPT][hapmap]
rs2107964	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs2158694	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs2260230	0.95[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2266922	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2283779	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2527683	0.87[ASN][1000 genomes]
rs2527684	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2527687	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2533878	0.95[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2533879	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2533882	0.87[EUR][1000 genomes]
rs2533884	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2644274	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2644275	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2644294	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2644295	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2644296	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2644297	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2644312	0.95[CEU][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs35957220	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6970963	0.84[ASN][1000 genomes]
rs709282	0.95[ASN][1000 genomes]
rs757791	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs7777484	0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7790322	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7807978	0.90[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs798480	0.93[ASN][1000 genomes]
rs798482	0.93[ASN][1000 genomes]
rs798485	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798486	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798487	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798488	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798489	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs798490	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798491	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798492	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs798493	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798495	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798496	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs798497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798498	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs798502	0.95[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs798503	0.81[CHB][hapmap]
rs798506	0.89[EUR][1000 genomes]
rs798508	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798511	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798512	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs798513	0.95[ASN][1000 genomes]
rs798514	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798518	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798526	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798528	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798531	0.95[ASN][1000 genomes]
rs798536	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798540	0.87[ASN][1000 genomes]
rs798544	0.84[ASN][1000 genomes]
rs798545	0.84[ASN][1000 genomes]
rs798546	0.84[ASN][1000 genomes]
rs798547	0.88[ASN][1000 genomes]
rs798548	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs798550	0.88[ASN][1000 genomes]
rs798551	0.88[ASN][1000 genomes]
rs798552	0.88[ASN][1000 genomes]
rs798554	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs798555	0.92[ASN][1000 genomes]
rs798556	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs798557	0.89[CHB][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs798558	0.88[ASN][1000 genomes]
rs798559	0.89[ASN][1000 genomes]
rs798560	0.89[ASN][1000 genomes]
rs798562	0.91[ASN][1000 genomes]
rs798565	0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs960273	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs798500	LOC392620	cis	multi-tissue	Pritchard
rs798500	GNA12	cis	multi-tissue	Pritchard
rs798500	GNA12	cis	Nerve Tibial	GTEx
rs798500	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 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	chr7:2775200-2791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:2775200-2796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:2775400-2797400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:2775400-2801200	Weak transcription	Primary T cells from cord blood	blood
14	chr7:2775800-2796400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:2775800-2796400	Weak transcription	HSMM	muscle
16	chr7:2776200-2797000	Weak transcription	Spleen	Spleen
17	chr7:2776800-2793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:2776800-2796200	Weak transcription	HepG2	liver
19	chr7:2777600-2796200	Weak transcription	Dnd41	blood
20	chr7:2778200-2796400	Weak transcription	Psoas Muscle	Psoas
21	chr7:2778600-2790800	Weak transcription	Adipose Nuclei	Adipose
22	chr7:2778600-2794800	Weak transcription	Primary B cells from cord blood	blood
23	chr7:2778600-2796200	Weak transcription	Fetal Lung	lung
24	chr7:2778600-2796400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:2778800-2795800	Weak transcription	Placenta	Placenta
26	chr7:2778800-2796200	Weak transcription	NHLF	lung
27	chr7:2779000-2796600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:2779600-2796000	Weak transcription	Fetal Intestine Small	intestine
29	chr7:2780200-2796200	Weak transcription	Fetal Stomach	stomach
30	chr7:2782800-2797000	Weak transcription	Right Ventricle	heart
31	chr7:2782800-2797200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:2783000-2795600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr7:2783000-2798000	Weak transcription	Lung	lung
34	chr7:2783600-2796800	Weak transcription	Fetal Intestine Large	intestine
35	chr7:2783800-2797200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:2787400-2796200	Weak transcription	HSMMtube	muscle
37	chr7:2788400-2797400	Weak transcription	Thymus	Thymus
38	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:2789600-2790800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:2789600-2791200	Enhancers	Colon Smooth Muscle	Colon
41	chr7:2789800-2790800	Enhancers	H1 Cell Line	embryonic stem cell
42	chr7:2789800-2791000	Enhancers	Gastric	stomach
43	chr7:2789800-2791000	Enhancers	Left Ventricle	heart
44	chr7:2789800-2791000	Enhancers	Ovary	ovary
45	chr7:2789800-2792200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr7:2790000-2791000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:2790000-2791400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr7:2790000-2791400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr7:2790000-2793200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:2790000-2793600	Weak transcription	Brain Inferior Temporal Lobe	brain

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