Variant report

Variant	rs7563706
Chromosome Location	chr2:54737729-54737730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10165490	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10180713	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs11892788	0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11898012	0.95[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12104998	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12105792	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12467581	0.82[EUR][1000 genomes]
rs12468469	0.83[EUR][1000 genomes]
rs12617036	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713260	0.83[EUR][1000 genomes]
rs13016942	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13399435	0.80[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1367295	0.95[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1541854	0.83[EUR][1000 genomes]
rs17344044	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17344072	0.91[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17521078	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1802889	0.81[JPT][hapmap]
rs1864493	0.95[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2941586	1.00[YRI][hapmap]
rs2941587	1.00[YRI][hapmap]
rs2941595	1.00[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2971877	1.00[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs2971879	1.00[ASW][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2971887	0.81[EUR][1000 genomes]
rs3796014	0.82[EUR][1000 genomes]
rs4233952	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4444573	0.84[EUR][1000 genomes]
rs4455199	0.84[EUR][1000 genomes]
rs4514917	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4519562	0.82[EUR][1000 genomes]
rs4592889	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671221	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671222	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671225	0.86[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671945	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671946	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671947	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671949	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671950	0.85[JPT][hapmap];0.89[TSI][hapmap]
rs4671951	1.00[ASW][hapmap];0.91[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671954	0.81[ASN][1000 genomes]
rs4671955	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671956	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.84[TSI][hapmap]
rs4990319	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545411	0.82[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545413	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545414	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545415	0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545418	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545419	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545420	0.82[EUR][1000 genomes]
rs6545427	0.86[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545429	0.95[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545434	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6704769	0.86[CEU][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6706372	0.83[EUR][1000 genomes]
rs6724590	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6729826	0.91[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6731661	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6732949	0.81[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6734658	0.83[EUR][1000 genomes]
rs6735813	0.83[EUR][1000 genomes]
rs6742607	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6746016	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6746306	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748816	0.82[EUR][1000 genomes]
rs6761369	0.95[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6761398	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558950	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589236	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7607451	0.83[EUR][1000 genomes]
rs907135	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7563706	EML6	cis	Thyroid	GTEx
rs7563706	C2orf73	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
4	chr2:54727600-54737800	Weak transcription	A549	lung
5	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
6	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54730600-54739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:54730600-54739200	Weak transcription	Spleen	Spleen
9	chr2:54730600-54739400	Weak transcription	HepG2	liver
10	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:54730800-54738600	Enhancers	Fetal Lung	lung
12	chr2:54732600-54738200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:54732800-54740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
15	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
16	chr2:54733600-54747000	Weak transcription	Gastric	stomach
17	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:54734600-54738400	Enhancers	Fetal Heart	heart
19	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:54735200-54738200	Enhancers	Right Atrium	heart
21	chr2:54735200-54740400	Enhancers	Left Ventricle	heart
22	chr2:54735400-54737800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:54735400-54738200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:54735400-54738200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:54735400-54738200	Enhancers	Right Ventricle	heart
26	chr2:54735600-54738400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54735600-54738400	Enhancers	Brain Cingulate Gyrus	brain
28	chr2:54735600-54738400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:54735600-54738600	Enhancers	Adipose Nuclei	Adipose
30	chr2:54735600-54738600	Enhancers	Brain Anterior Caudate	brain
31	chr2:54735600-54740800	Enhancers	Brain Angular Gyrus	brain
32	chr2:54735800-54738200	Enhancers	Stomach Smooth Muscle	stomach
33	chr2:54735800-54740600	Enhancers	Brain Hippocampus Middle	brain
34	chr2:54735800-54741000	Enhancers	Brain Substantia Nigra	brain
35	chr2:54736200-54738200	Enhancers	Psoas Muscle	Psoas
36	chr2:54736600-54738200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:54736600-54738400	Enhancers	HSMMtube	muscle
38	chr2:54736600-54740800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:54736800-54737800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:54736800-54737800	Enhancers	Placenta	Placenta
41	chr2:54736800-54738200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:54736800-54738200	Enhancers	Liver	Liver
43	chr2:54736800-54738200	Enhancers	Colon Smooth Muscle	Colon
44	chr2:54736800-54738200	Enhancers	Fetal Muscle Leg	muscle
45	chr2:54736800-54738400	Enhancers	Ovary	ovary
46	chr2:54737000-54737800	Enhancers	Fetal Thymus	thymus
47	chr2:54737000-54738200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
49	chr2:54737200-54738400	Enhancers	Primary hematopoietic stem cells	blood
50	chr2:54737400-54737800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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