Variant report

Variant	rs13227219
Chromosome Location	chr7:65844062-65844063
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1002053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10215948	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10257427	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10261398	0.85[CHB][hapmap]
rs10267430	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10282433	0.85[CHB][hapmap]
rs10755833	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11765965	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532998	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12533997	0.82[ASN][1000 genomes]
rs12535036	0.82[ASN][1000 genomes]
rs12537823	0.85[CHB][hapmap]
rs12668936	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12673810	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12698520	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12698521	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12698523	0.82[ASN][1000 genomes]
rs13309022	0.82[ASN][1000 genomes]
rs1363055	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1643395	0.90[ASN][1000 genomes]
rs1695815	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807064	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1833495	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1968225	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1974769	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2036264	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2042133	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2077593	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2161065	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2173570	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2277911	0.83[ASN][1000 genomes]
rs2420591	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2420599	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34406470	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35149210	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3735148	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3935391	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4149461	0.85[CHB][hapmap]
rs4236208	0.85[CHB][hapmap]
rs4717292	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4717299	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4717300	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4718343	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718344	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718349	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4718357	0.83[ASN][1000 genomes]
rs55748098	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60193905	0.82[ASN][1000 genomes]
rs6460291	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6460292	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460295	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460296	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460300	0.83[ASN][1000 genomes]
rs6945019	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6945032	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6945843	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6949920	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6956179	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6959268	0.85[CHB][hapmap]
rs6960476	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6961155	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6961990	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6962717	0.84[CHB][hapmap]
rs6963646	0.87[CEU][hapmap]
rs6970357	0.80[ASN][1000 genomes]
rs6971509	0.87[CEU][hapmap]
rs6978429	0.84[ASN][1000 genomes]
rs6979382	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709595	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709596	0.82[AFR][1000 genomes]
rs709597	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781061	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7781698	0.83[ASN][1000 genomes]
rs7783613	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778682	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs778685	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778689	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778692	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778694	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778695	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs778699	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778700	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778706	0.84[CEU][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778708	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778709	0.82[EUR][1000 genomes]
rs778710	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778712	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778721	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778722	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs778723	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778726	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778727	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs778731	0.89[ASN][1000 genomes]
rs778735	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7788984	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7789554	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7789768	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7791891	0.88[ASN][1000 genomes]
rs7794930	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7799834	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7803416	0.83[ASN][1000 genomes]
rs7803424	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs937495	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9691480	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9791895	0.83[ASN][1000 genomes]
rs9969301	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS 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 miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv970513	chr7:65842694-65860742	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv981506	chr7:65842694-65876873	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv32937	chr7:65842976-65844524	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs13227219	GS1-124K5.4	cis	Whole Blood	GTEx
rs13227219	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs13227219	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13227219	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs13227219	RP4-756H11.3	cis	Thyroid	GTEx
rs13227219	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs13227219	RP4-756H11.3	cis	Artery Tibial	GTEx
rs13227219	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs13227219	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs13227219	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13227219	RP4-756H11.3	cis	lung	GTEx
rs13227219	RNU6-96P	cis	Thyroid	GTEx
rs13227219	RP4-756H11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
2	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
3	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:65825000-65844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:65825200-65844200	Weak transcription	NHLF	lung
6	chr7:65831800-65844200	Weak transcription	NHDF-Ad	bronchial
7	chr7:65832000-65844200	Weak transcription	Fetal Lung	lung
8	chr7:65836600-65846400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:65838800-65844600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:65839000-65844800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:65839400-65844400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:65839400-65844600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:65839800-65844200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:65839800-65844200	Weak transcription	Brain Anterior Caudate	brain
15	chr7:65839800-65845200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:65840000-65878400	Weak transcription	Psoas Muscle	Psoas
17	chr7:65840200-65844800	Strong transcription	Fetal Muscle Leg	muscle
18	chr7:65840400-65844400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr7:65840400-65844400	Weak transcription	HepG2	liver
20	chr7:65840400-65873400	Weak transcription	K562	blood
21	chr7:65840600-65858400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr7:65841200-65844200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:65841200-65844400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:65841200-65847600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:65841400-65844200	Weak transcription	Left Ventricle	heart
26	chr7:65841400-65875400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:65841600-65845000	Strong transcription	Right Ventricle	heart
28	chr7:65841800-65844600	Weak transcription	Primary B cells from cord blood	blood
29	chr7:65841800-65844800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:65841800-65845400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:65842200-65844200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:65842200-65844400	Strong transcription	Spleen	Spleen
33	chr7:65842400-65844200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:65842400-65844400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:65842400-65844400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:65842400-65845000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:65842400-65867800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:65842600-65844400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr7:65842600-65844800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:65842600-65845400	Strong transcription	Fetal Intestine Large	intestine
41	chr7:65842600-65845400	Strong transcription	Pancreas	Pancrea
42	chr7:65842600-65845600	Strong transcription	Gastric	stomach
43	chr7:65842600-65846800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr7:65842800-65844400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:65842800-65844400	Weak transcription	A549	lung
46	chr7:65842800-65845000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:65842800-65845600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:65842800-65845600	Strong transcription	Brain Hippocampus Middle	brain
49	chr7:65842800-65845800	Strong transcription	Liver	Liver
50	chr7:65843000-65844200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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