Variant report

Variant	rs1259338
Chromosome Location	chr3:120165614-120165615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1123897	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs1123898	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1147706	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1147709	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1147710	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1147717	0.81[ASN][1000 genomes]
rs1147720	0.88[CHB][hapmap]
rs1259311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259318	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1259329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1259332	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1259333	0.85[JPT][hapmap]
rs1259334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259335	0.83[JPT][hapmap]
rs1259336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1259339	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1259457	0.81[ASN][1000 genomes]
rs1259471	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259472	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259473	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1267675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1270209	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520881	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1716835	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1716837	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733298	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733299	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1733301	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733303	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733304	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733306	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733307	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1982186	0.81[ASN][1000 genomes]
rs2252084	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2700263	0.90[ASN][1000 genomes]
rs2702155	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5000757	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6768839	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs735138	0.82[EUR][1000 genomes]
rs874477	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs874478	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs874479	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs874480	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9631455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3499188	chr3:120160412-120166010	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv436396	chr3:120160617-120166439	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3499192	chr3:120160812-120165910	Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3324710	chr3:120161962-120166460	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1259338	NR1I2	cis	cerebellum	SCAN
rs1259338	FSTL1	cis	cerebellum	SCAN
rs1259338	FSTL1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:120138200-120169200	Weak transcription	Gastric	stomach
3	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
5	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:120153000-120167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:120155800-120168400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120156200-120166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:120156600-120168800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:120156800-120166000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:120158000-120166200	Weak transcription	Fetal Brain Female	brain
12	chr3:120158000-120167600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:120158200-120167400	Weak transcription	Brain Germinal Matrix	brain
14	chr3:120158800-120166000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:120158800-120167400	Weak transcription	A549	lung
16	chr3:120159600-120165800	Weak transcription	Spleen	Spleen
17	chr3:120160000-120167400	Weak transcription	HMEC	breast
18	chr3:120160000-120167600	Weak transcription	NHEK	skin
19	chr3:120160400-120165800	Weak transcription	Placenta	Placenta
20	chr3:120160600-120165800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:120160600-120166000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:120160600-120167400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:120160800-120166000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:120160800-120166000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:120160800-120166200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:120160800-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:120160800-120167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:120161000-120166000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:120161000-120167400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:120161200-120166000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:120161200-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:120161400-120165800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:120162200-120165800	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr3:120162200-120166800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:120162200-120166800	Genic enhancers	NH-A	brain
36	chr3:120162200-120168800	Weak transcription	Esophagus	oesophagus
37	chr3:120162600-120165800	Weak transcription	Fetal Brain Male	brain
38	chr3:120162800-120166000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:120163000-120169000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:120163200-120166400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:120163800-120165800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:120163800-120166000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:120163800-120166600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
44	chr3:120163800-120167800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:120164600-120165800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:120164600-120165800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:120164600-120166400	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:120164600-120166400	Genic enhancers	Ovary	ovary
49	chr3:120164600-120166600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:120164600-120166600	Enhancers	Aorta	Aorta

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