Variant report

Variant	rs6493858
Chromosome Location	chr15:56736478-56736479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11630363	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633374	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855094	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs12900678	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12905782	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs12908734	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1402177	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1477590	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1549452	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554410	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16976890	0.91[CHB][hapmap]
rs1711481	0.83[EUR][1000 genomes]
rs17819438	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2114183	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2249090	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap]
rs2303441	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460646	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2460650	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs2554287	0.91[CHB][hapmap]
rs2682019	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2682021	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2682023	0.83[EUR][1000 genomes]
rs2682051	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs2682053	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2682054	0.96[CEU][hapmap]
rs2682059	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs2713933	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2713936	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2718901	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2718908	0.81[EUR][1000 genomes]
rs2718921	0.91[CHB][hapmap]
rs2718934	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs2725854	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap]
rs2725856	0.82[CHB][hapmap]
rs2725862	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2947021	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34755898	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35497167	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35863560	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784552	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3817406	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3985758	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774859	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022122	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62022127	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62022133	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493856	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7170307	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7174892	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181235	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7181320	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7496402	0.90[EUR][1000 genomes]
rs795790	0.80[CEU][hapmap]
rs795791	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs795797	0.92[AFR][1000 genomes]
rs795800	0.89[ASW][hapmap];0.91[CHB][hapmap];0.87[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv35150	chr15:56677730-56896304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv9270	chr15:56686946-56760420	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2757602	chr15:56736478-56790080	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2760033	chr15:56736478-56790080	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Relative hand skill in reading disability	24068947	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493858	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56690000-56737800	Weak transcription	Stomach Mucosa	stomach
2	chr15:56716000-56756600	Weak transcription	HSMM	muscle
3	chr15:56718600-56736600	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:56718600-56756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:56719200-56742400	Weak transcription	Fetal Intestine Large	intestine
6	chr15:56719400-56736800	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:56720800-56740600	Weak transcription	GM12878-XiMat	blood
8	chr15:56721400-56737600	Weak transcription	Pancreas	Pancrea
9	chr15:56721800-56736600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:56722400-56736800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:56722800-56746800	Weak transcription	Thymus	Thymus
12	chr15:56723400-56756600	Weak transcription	Fetal Stomach	stomach
13	chr15:56723600-56737400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:56731000-56738600	Strong transcription	Dnd41	blood
15	chr15:56732200-56756800	Weak transcription	Fetal Brain Male	brain
16	chr15:56732800-56742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:56733000-56739800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:56734600-56736800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:56734800-56751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:56735000-56738200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:56735000-56738400	Strong transcription	Fetal Lung	lung
22	chr15:56735000-56739600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:56735000-56739800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:56735200-56740200	Weak transcription	Osteobl	bone
25	chr15:56735200-56756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:56735400-56736800	Weak transcription	Ovary	ovary
27	chr15:56735400-56739800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:56735400-56756600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:56735600-56737400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr15:56735600-56756400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:56735600-56756600	Weak transcription	Brain Anterior Caudate	brain
32	chr15:56736000-56751200	Weak transcription	Fetal Thymus	thymus
33	chr15:56736200-56736800	Strong transcription	Fetal Kidney	kidney
34	chr15:56736400-56755200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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