Variant report

Variant	rs1513609
Chromosome Location	chr1:227381953-227381954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10127638	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10495256	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs12118840	1.00[JPT][hapmap]
rs12403775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1319103	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1929855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2297418	0.93[CHB][hapmap]
rs2670470	0.83[EUR][1000 genomes]
rs2718191	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718214	0.83[EUR][1000 genomes]
rs2718220	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2718223	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2813955	0.92[EUR][1000 genomes]
rs2813956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2813957	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813977	0.84[AFR][1000 genomes]
rs2953640	0.90[ASW][hapmap];0.94[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs3768437	0.87[AMR][1000 genomes]
rs4146588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4375224	0.83[EUR][1000 genomes]
rs4653822	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6426578	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6426596	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6677602	0.86[CHB][hapmap]
rs66796195	0.90[EUR][1000 genomes]
rs72750169	0.82[AMR][1000 genomes]
rs72750202	0.82[AMR][1000 genomes]
rs72753628	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72755321	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531992	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7540155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7540391	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7540618	0.91[EUR][1000 genomes]
rs7541033	0.93[CHB][hapmap]
rs938257	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]

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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1513609	AIDA	cis	cerebellum	SCAN
rs1513609	WNT9A	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:227343200-227400400	Weak transcription	A549	lung
4	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
7	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
16	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
17	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
18	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
19	chr1:227369200-227382600	Weak transcription	Fetal Brain Female	brain
20	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:227373400-227397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
24	chr1:227374800-227391000	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:227375200-227386800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:227375600-227410800	Weak transcription	HepG2	liver
27	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
28	chr1:227377000-227388800	Weak transcription	Small Intestine	intestine
29	chr1:227378000-227389400	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:227378400-227401000	Weak transcription	Placenta	Placenta
31	chr1:227379000-227398000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:227379000-227398000	Weak transcription	Liver	Liver
33	chr1:227379600-227399200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:227380200-227385800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:227380200-227385800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:227380200-227391200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:227380200-227402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:227380200-227405200	Weak transcription	Gastric	stomach
39	chr1:227380200-227421800	Weak transcription	Ovary	ovary
40	chr1:227380400-227382200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:227380400-227382600	Strong transcription	K562	blood
42	chr1:227380400-227385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:227380400-227385400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:227380400-227385800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227380400-227385800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:227380400-227385800	Weak transcription	HSMM	muscle
47	chr1:227380400-227389000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:227380400-227389400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:227380400-227398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:227380400-227398000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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