Variant report

Variant	rs7302700
Chromosome Location	chr12:29628628-29628629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10161540	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10219521	0.90[EUR][1000 genomes]
rs10219541	0.90[EUR][1000 genomes]
rs11050231	0.90[EUR][1000 genomes]
rs11050232	0.85[EUR][1000 genomes]
rs11050234	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11050237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050242	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11050243	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11050247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11610605	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11611065	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611499	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614232	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11614288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614744	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11829375	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11829418	0.83[TSI][hapmap]
rs11831164	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11831165	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11833098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11838057	0.90[EUR][1000 genomes]
rs1369899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1436314	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2042512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288127	0.86[CHB][hapmap]
rs2350531	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28560462	1.00[ASN][1000 genomes]
rs34137040	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35198374	1.00[ASN][1000 genomes]
rs35494573	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741751	0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3764951	0.86[CHB][hapmap]
rs3782512	0.86[CHB][hapmap]
rs4280037	0.86[CHB][hapmap]
rs56179940	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241141	1.00[ASN][1000 genomes]
rs56808425	0.89[EUR][1000 genomes]
rs58171188	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58359809	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59273552	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487826	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487827	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7138160	0.86[CHB][hapmap]
rs7138552	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294517	0.86[CHB][hapmap]
rs7295922	0.93[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7296302	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7296554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297234	1.00[ASN][1000 genomes]
rs7297659	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7301354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7302425	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7302549	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7306407	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7309876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7311051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311329	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7312547	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7312776	0.82[ASN][1000 genomes]
rs7313103	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7313307	1.00[ASN][1000 genomes]
rs73276833	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73276902	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73278706	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73278726	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73278734	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73278736	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73278740	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7489238	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953237	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7954043	0.90[EUR][1000 genomes]
rs7963197	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7964648	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964728	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964979	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7965132	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7965185	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7975356	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7977826	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978026	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs878837	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs880267	0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7302700	FAR2	cis	parietal	SCAN
rs7302700	SLC24A6	trans	brain	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29584200-29641800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:29588000-29639800	Weak transcription	Aorta	Aorta
3	chr12:29598400-29657400	Weak transcription	HSMM	muscle
4	chr12:29600000-29639800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:29600600-29675600	Weak transcription	Psoas Muscle	Psoas
6	chr12:29604200-29655400	Weak transcription	Adipose Nuclei	Adipose
7	chr12:29609400-29631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:29612800-29655600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:29613600-29655600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:29613600-29666800	Weak transcription	Spleen	Spleen
11	chr12:29614600-29658000	Weak transcription	HSMMtube	muscle
12	chr12:29616400-29659400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:29617400-29657400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:29618200-29642000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:29624000-29630800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:29625000-29656800	Weak transcription	Left Ventricle	heart
17	chr12:29627200-29639800	Weak transcription	Brain Anterior Caudate	brain
18	chr12:29628000-29662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:29628200-29629000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:29628600-29634800	Weak transcription	Right Ventricle	heart

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