Variant report

Variant	rs2579515
Chromosome Location	chr2:96686723-96686724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10183151	0.87[CEU][hapmap]
rs11680950	0.89[YRI][hapmap]
rs11683523	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11687113	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1168965	0.86[CEU][hapmap]
rs1168968	0.81[CEU][hapmap]
rs1168970	0.82[CEU][hapmap]
rs1168974	0.81[CEU][hapmap];0.89[YRI][hapmap]
rs1168975	0.82[CEU][hapmap];0.89[YRI][hapmap]
rs1168976	0.81[CEU][hapmap];0.89[YRI][hapmap]
rs11689832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11695514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2229169	0.91[CEU][hapmap]
rs2312955	0.81[CEU][hapmap]
rs2438972	0.92[CEU][hapmap]
rs2438978	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2462774	0.94[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2462776	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2579517	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2579518	0.81[EUR][1000 genomes]
rs2579519	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2692893	0.95[CEU][hapmap];0.89[YRI][hapmap]
rs2692894	0.86[CEU][hapmap]
rs2692954	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918816	0.87[ASN][1000 genomes]
rs2918929	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2969473	0.80[EUR][1000 genomes]
rs2969475	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2969477	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2969491	0.87[CEU][hapmap]
rs4144055	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs4426564	0.81[CEU][hapmap]
rs4527246	0.92[CEU][hapmap]
rs4907226	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4907288	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4907299	0.81[CEU][hapmap]
rs62155508	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62155510	0.92[ASN][1000 genomes]
rs62155511	0.89[ASN][1000 genomes]
rs6740563	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs72492201	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7604842	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv874669	chr2:96547820-96691125	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv870250	chr2:96610946-96739308	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1837811	chr2:96622689-96730375	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv874670	chr2:96637870-96693357	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv874671	chr2:96637870-96727850	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv874674	chr2:96651163-96741944	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv1836563	chr2:96669134-96730375	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv993391	chr2:96671521-96731854	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv961454	chr2:96677855-96701857	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2579515	FAHD2CP	cis	Muscle Skeletal	GTEx
rs2579515	GPAT2	cis	Muscle Skeletal	GTEx
rs2579515	FAHD2CP	cis	lung	GTEx
rs2579515	ADRA2B	cis	Thyroid	GTEx
rs2579515	GPAT2	cis	Adipose Subcutaneous	GTEx
rs2579515	ADRA2B	cis	Nerve Tibial	GTEx
rs2579515	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs2579515	FAHD2CP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96675600-96691400	Weak transcription	Gastric	stomach
2	chr2:96675800-96689000	Weak transcription	Spleen	Spleen
3	chr2:96676400-96688400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:96677000-96688200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:96677000-96688200	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:96677000-96688400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:96677000-96690200	Weak transcription	Right Ventricle	heart
8	chr2:96677000-96690400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:96677200-96688200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:96677200-96688800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:96678600-96691000	Weak transcription	Left Ventricle	heart
12	chr2:96678800-96690800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:96679800-96687000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:96679800-96688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:96679800-96690000	Weak transcription	Fetal Stomach	stomach
16	chr2:96685600-96688400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:96685600-96688400	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:96685600-96688600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:96685600-96690200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:96685600-96690800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:96686600-96688200	Weak transcription	Brain Substantia Nigra	brain
22	chr2:96686600-96688400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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