Variant report

Variant	rs2303122
Chromosome Location	chr5:52379277-52379278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52372459..52375173-chr5:52375877..52379453,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1062535	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1126643	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12515364	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518279	0.85[ASN][1000 genomes]
rs12521915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12652168	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1421929	0.84[ASN][1000 genomes]
rs1421930	0.84[ASN][1000 genomes]
rs1421931	0.84[ASN][1000 genomes]
rs1421932	0.84[ASN][1000 genomes]
rs1833558	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1862191	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1991013	0.87[ASN][1000 genomes]
rs2075615	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075616	0.83[ASN][1000 genomes]
rs2075617	0.82[ASN][1000 genomes]
rs2287871	0.84[ASN][1000 genomes]
rs2303123	0.93[ASN][1000 genomes]
rs2303127	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2897458	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910964	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910965	0.84[ASN][1000 genomes]
rs2910971	0.84[ASN][1000 genomes]
rs2974976	0.84[ASN][1000 genomes]
rs2974978	0.84[ASN][1000 genomes]
rs2974987	0.84[ASN][1000 genomes]
rs3212424	0.83[CEU][hapmap]
rs3212467	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212472	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3212508	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212509	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212522	0.84[ASN][1000 genomes]
rs3212527	0.84[ASN][1000 genomes]
rs3212533	0.84[ASN][1000 genomes]
rs3212591	0.85[ASN][1000 genomes]
rs3212600	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212601	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212619	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212640	0.87[ASN][1000 genomes]
rs3797495	0.83[CEU][hapmap]
rs3797498	0.83[CEU][hapmap]
rs67719154	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6880055	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6898333	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7725246	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs984966	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989073	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs990602	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv880598	chr5:52379277-52382904	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2303122	SNX18	cis	cerebellum	SCAN
rs2303122	DHX29	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
3	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:52341200-52396400	Strong transcription	HMEC	breast
6	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52342600-52383800	Strong transcription	NHEK	skin
8	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
9	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
11	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
12	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:52349400-52379600	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
16	chr5:52359400-52380000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
19	chr5:52362200-52387800	Strong transcription	HepG2	liver
20	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
23	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
25	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:52367600-52381200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:52367800-52386000	Strong transcription	NH-A	brain
29	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
30	chr5:52369000-52381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:52369400-52382600	Weak transcription	Brain Angular Gyrus	brain
33	chr5:52369400-52383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:52369800-52379800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
37	chr5:52372000-52382600	Weak transcription	Brain Anterior Caudate	brain
38	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
39	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:52372200-52382600	Weak transcription	Lung	lung
41	chr5:52372200-52382800	Weak transcription	Spleen	Spleen
42	chr5:52372200-52384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:52372200-52394800	Weak transcription	Gastric	stomach
45	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
46	chr5:52372400-52385000	Weak transcription	Osteobl	bone
47	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
49	chr5:52373000-52385600	Weak transcription	Ovary	ovary
50	chr5:52373000-52387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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