Variant report

Variant	rs798488
Chromosome Location	chr7:2802522-2802523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:2802153-2802805	U87	brain:	n/a	n/a
2	POLR2A	chr7:2802023-2803461	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr7:2802177-2803615	IMR90	lung:	n/a	n/a
4	TAF1	chr7:2802132-2802628	PFSK-1	brain:	n/a	n/a
5	TAF1	chr7:2802310-2802560	PFSK-1	brain:	n/a	n/a
6	MAZ	chr7:2801882-2803312	IMR90	lung:	n/a	n/a
7	RAD21	chr7:2802379-2803162	IMR90	lung:	n/a	chr7:2802646-2802660
8	MXI1	chr7:2801857-2803591	IMR90	lung:	n/a	n/a
9	POLR2A	chr7:2802147-2802888	U87	brain:	n/a	n/a
10	POLR2A	chr7:2802103-2803400	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr7:2802344-2802673	U87	brain:	n/a	n/a
12	FOXP2	chr7:2802268-2802743	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr7:2802302-2802707	U87	brain:	n/a	n/a
14	POLR2A	chr7:2802306-2802648	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr7:2802349-2802565	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:2801788..2804432-chr7:2882018..2884117,3	K562	blood:

Variant related genes	Relation type
AMZ1	TF binding region
GNA12	TF binding region
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1182172	0.83[EUR][1000 genomes]
rs1182174	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182176	0.85[EUR][1000 genomes]
rs1182177	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1182178	0.85[EUR][1000 genomes]
rs1182179	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182181	0.95[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs1182182	0.85[EUR][1000 genomes]
rs1182183	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182184	0.84[EUR][1000 genomes]
rs1182185	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1182186	0.85[EUR][1000 genomes]
rs1182187	0.87[EUR][1000 genomes]
rs1182188	0.95[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1182189	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1182196	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs1182198	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1182199	0.80[EUR][1000 genomes]
rs1182207	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1182208	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1182209	0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs1183085	0.86[EUR][1000 genomes]
rs13243214	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1636255	0.81[CEU][hapmap]
rs1636264	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs1713919	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs2107964	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2158694	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs2248390	0.81[ASN][1000 genomes]
rs2251491	0.81[ASN][1000 genomes]
rs2260230	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2266922	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2283779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2283783	0.81[ASN][1000 genomes]
rs2283784	0.81[ASN][1000 genomes]
rs2527683	0.90[ASN][1000 genomes]
rs2527684	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2527687	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2527690	0.82[ASN][1000 genomes]
rs2527692	0.81[ASN][1000 genomes]
rs2533878	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2533879	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2533882	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2533884	0.92[EUR][1000 genomes]
rs2644274	0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2644275	0.89[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2644294	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2644295	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2644296	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2644297	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs2644312	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35957220	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6970963	0.88[ASN][1000 genomes]
rs6978692	0.81[ASN][1000 genomes]
rs709282	0.89[ASN][1000 genomes]
rs757791	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs7777484	0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7807978	0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs798480	0.99[ASN][1000 genomes]
rs798481	0.83[ASN][1000 genomes]
rs798482	0.99[ASN][1000 genomes]
rs798485	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798487	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs798489	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs798490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798491	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798492	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs798493	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798494	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798495	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798496	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798497	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798498	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798499	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs798500	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]
rs798502	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs798506	0.88[EUR][1000 genomes]
rs798508	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798511	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798512	0.84[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs798513	0.89[ASN][1000 genomes]
rs798514	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798518	0.86[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798526	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798528	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798531	0.89[ASN][1000 genomes]
rs798536	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798540	0.80[ASN][1000 genomes]
rs798547	0.82[ASN][1000 genomes]
rs798548	0.91[CEU][hapmap]
rs798550	0.82[ASN][1000 genomes]
rs798551	0.82[ASN][1000 genomes]
rs798552	0.82[ASN][1000 genomes]
rs798554	0.86[CEU][hapmap];0.82[ASN][1000 genomes]
rs798555	0.85[ASN][1000 genomes]
rs798556	0.86[CEU][hapmap];0.82[ASN][1000 genomes]
rs798557	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs798558	0.82[ASN][1000 genomes]
rs798559	0.82[ASN][1000 genomes]
rs798560	0.82[ASN][1000 genomes]
rs798562	0.84[ASN][1000 genomes]
rs960273	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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
rs798488		cis	Lymphoblastoid	GTEx
rs798488	GNA12	cis	multi-tissue	Pritchard
rs798488	GNA12	cis	Nerve Tibial	GTEx
rs798488	LOC392620	cis	multi-tissue	Pritchard
rs798488	GNA12	Cis_1M	lymphoblastoid	RTeQTL
rs798488	GNA12	cis	Esophagus Muscularis	GTEx
rs798488	GNA12	cis	Artery Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2789200-2831600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:2790000-2830400	Weak transcription	Aorta	Aorta
3	chr7:2791200-2803400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:2796400-2803200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr7:2796400-2804000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr7:2796800-2803600	Weak transcription	Primary B cells from cord blood	blood
7	chr7:2796800-2804400	Enhancers	Fetal Muscle Leg	muscle
8	chr7:2797000-2803200	Enhancers	Right Ventricle	heart
9	chr7:2797000-2803800	Enhancers	Brain Cingulate Gyrus	brain
10	chr7:2797000-2805400	Enhancers	Placenta	Placenta
11	chr7:2797600-2831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:2798000-2803600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr7:2798000-2827400	Weak transcription	Thymus	Thymus
14	chr7:2798200-2803200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:2798400-2803000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:2799000-2803800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr7:2799200-2802600	Enhancers	Left Ventricle	heart
18	chr7:2799200-2804400	Enhancers	Ovary	ovary
19	chr7:2799200-2804600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:2799200-2817000	Weak transcription	Dnd41	blood
21	chr7:2799200-2827200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:2799600-2803800	Genic enhancers	Fetal Stomach	stomach
23	chr7:2799600-2807600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:2799600-2825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:2800200-2803600	Enhancers	Fetal Heart	heart
26	chr7:2800200-2806400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:2800200-2815800	Weak transcription	Liver	Liver
28	chr7:2800400-2804400	Enhancers	NHDF-Ad	bronchial
29	chr7:2800400-2810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:2800600-2802800	Enhancers	Brain Substantia Nigra	brain
31	chr7:2800600-2802800	Weak transcription	Fetal Brain Female	brain
32	chr7:2800600-2803800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:2800600-2804600	Enhancers	Fetal Muscle Trunk	muscle
34	chr7:2800800-2802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:2800800-2802800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:2800800-2802800	Enhancers	Colon Smooth Muscle	Colon
37	chr7:2800800-2803000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:2800800-2803800	Enhancers	Brain Angular Gyrus	brain
39	chr7:2800800-2805600	Weak transcription	GM12878-XiMat	blood
40	chr7:2800800-2808000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:2800800-2817200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr7:2800800-2818200	Weak transcription	Hela-S3	cervix
43	chr7:2801000-2802800	Weak transcription	A549	lung
44	chr7:2801000-2803000	Weak transcription	Fetal Thymus	thymus
45	chr7:2801000-2803800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr7:2801000-2808600	Weak transcription	Brain Germinal Matrix	brain
47	chr7:2801000-2810200	Weak transcription	Gastric	stomach
48	chr7:2801000-2810200	Weak transcription	K562	blood
49	chr7:2801000-2811000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:2801000-2812800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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