Variant report

Variant	rs13242216
Chromosome Location	chr7:65898277-65898278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10247526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10807701	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10807702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10950032	0.85[EUR][1000 genomes]
rs12530490	0.85[EUR][1000 genomes]
rs1267820	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13232193	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13235972	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392104	0.85[EUR][1000 genomes]
rs1499613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1499614	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1532573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1553174	0.85[EUR][1000 genomes]
rs1618893	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1638736	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1979823	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs34192067	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34363376	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34700450	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34807232	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35823062	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36104268	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4149468	0.84[EUR][1000 genomes]
rs4481472	0.82[EUR][1000 genomes]
rs4718333	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs58669269	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6958420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6964245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7778911	0.85[EUR][1000 genomes]
rs778679	0.88[EUR][1000 genomes]
rs778683	0.85[EUR][1000 genomes]
rs778687	0.85[EUR][1000 genomes]
rs778691	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778693	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778698	0.84[ASN][1000 genomes]
rs778701	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778704	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs778732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs778733	0.85[EUR][1000 genomes]
rs7792391	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7804223	0.82[EUR][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	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv970867	chr7:65893874-65900243	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13242216	ASL	cis	multi-tissue	Pritchard
rs13242216	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13242216	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13242216	RP4-756H11.3	cis	lung	GTEx
rs13242216	GUSB	cis	Whole Blood	GTEx
rs13242216	VKORC1L1	cis	Whole Blood	GTEx
rs13242216	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879000-65905600	Weak transcription	Lung	lung
2	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
4	chr7:65879200-65902000	Weak transcription	Brain Substantia Nigra	brain
5	chr7:65879200-65904000	Weak transcription	Fetal Lung	lung
6	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
7	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
8	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:65879200-65946000	Weak transcription	NHEK	skin
10	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
11	chr7:65879400-65900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:65879400-65901000	Weak transcription	Brain Angular Gyrus	brain
13	chr7:65879400-65901200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
16	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
17	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
20	chr7:65879600-65899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:65879600-65900600	Weak transcription	Brain Germinal Matrix	brain
22	chr7:65879600-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:65879600-65920400	Weak transcription	Primary B cells from cord blood	blood
26	chr7:65879800-65913600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:65884000-65919600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:65885000-65904200	Weak transcription	K562	blood
29	chr7:65886000-65913600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:65886600-65920400	Weak transcription	Right Ventricle	heart
31	chr7:65887000-65924600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:65887000-65924600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:65887200-65904600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:65889200-65903000	Weak transcription	Thymus	Thymus
35	chr7:65889200-65939600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:65889600-65913800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:65890000-65928800	Weak transcription	Adipose Nuclei	Adipose
38	chr7:65890200-65907400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:65890400-65916200	Weak transcription	Fetal Thymus	thymus
40	chr7:65891400-65902000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:65891600-65939000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:65892000-65931800	Weak transcription	Ovary	ovary
43	chr7:65893200-65913400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:65894200-65899800	Weak transcription	Spleen	Spleen
45	chr7:65894200-65905400	Weak transcription	Gastric	stomach
46	chr7:65894200-65939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:65894600-65899400	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:65894600-65905200	Weak transcription	Pancreas	Pancrea
49	chr7:65894800-65914000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr7:65895000-65899400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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