Variant report

Variant	rs460428
Chromosome Location	chr22:29970989-29970990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29968594..29971400-chr22:29974494..29977616,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184117	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1006396	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10427559	0.80[EUR][1000 genomes]
rs10427614	0.80[EUR][1000 genomes]
rs1049534	0.89[ASW][hapmap];0.85[CEU][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11704049	0.80[EUR][1000 genomes]
rs11705569	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12628784	0.81[EUR][1000 genomes]
rs165625	0.80[CEU][hapmap]
rs16987832	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs16987839	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs174650	0.80[CEU][hapmap]
rs2009354	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs2074948	0.89[ASW][hapmap];0.90[CEU][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2074951	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs2188120	0.89[ASW][hapmap];0.90[CEU][hapmap];0.84[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2240637	0.84[EUR][1000 genomes]
rs2247753	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2262240	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302141	0.89[ASW][hapmap];0.90[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2530656	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2530658	0.84[ASN][1000 genomes]
rs2530664	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2531848	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs425992	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs433194	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs456285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs456585	0.88[ASN][1000 genomes]
rs457295	0.85[EUR][1000 genomes]
rs457335	0.85[EUR][1000 genomes]
rs458196	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs459351	0.85[EUR][1000 genomes]
rs459450	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4608625	0.82[EUR][1000 genomes]
rs460994	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs462444	0.88[ASW][hapmap];0.95[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];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs463220	0.90[ASN][1000 genomes]
rs467555	0.80[EUR][1000 genomes]
rs467902	0.85[EUR][1000 genomes]
rs467912	0.85[EUR][1000 genomes]
rs468019	0.87[EUR][1000 genomes]
rs468224	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs468254	0.88[ASN][1000 genomes]
rs468356	0.85[EUR][1000 genomes]
rs468475	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468692	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468795	0.81[ASN][1000 genomes]
rs468852	0.88[ASN][1000 genomes]
rs469230	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469253	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469295	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469363	0.89[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469565	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752933	0.80[CEU][hapmap]
rs5752940	0.84[EUR][1000 genomes]
rs5763241	0.84[YRI][hapmap]
rs5763286	0.90[CEU][hapmap]
rs5763297	0.89[ASW][hapmap];0.90[CEU][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs5763300	0.83[EUR][1000 genomes]
rs5763301	0.89[ASW][hapmap];0.90[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs5763303	0.90[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs5763305	0.87[JPT][hapmap];0.82[TSI][hapmap]
rs5763306	0.90[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs5763349	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs695525	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs695668	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs695780	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs695816	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73159006	0.82[EUR][1000 genomes]
rs73159040	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7609	0.90[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8135828	0.87[JPT][hapmap];0.82[TSI][hapmap]
rs8141518	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs460428	NIPSNAP1	cis	cerebellum	SCAN
rs460428	ASCC2	cis	cerebellum	SCAN
rs460428	CABP7	cis	cerebellum	SCAN
rs460428	RNF185	cis	cerebellum	SCAN
rs460428	THOC5	cis	Thyroid	GTEx
rs460428	THOC5	cis	cerebellum	SCAN
rs460428	THOC5	cis	Artery Aorta	GTEx
rs460428	THOC5	cis	lung	GTEx
rs460428	THOC5	cis	Muscle Skeletal	GTEx
rs460428	CRYBB3	cis	cerebellum	SCAN
rs460428	THOC5	cis	Adipose Subcutaneous	GTEx
rs460428	THOC5	cis	Esophagus Muscularis	GTEx
rs460428	THOC5	cis	Nerve Tibial	GTEx
rs460428	THOC5	cis	Artery Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29950200-29976000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29950400-29976200	Weak transcription	HMEC	breast
3	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr22:29951200-29971400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:29951600-29971600	Strong transcription	Fetal Stomach	stomach
7	chr22:29952000-29976400	Weak transcription	Right Atrium	heart
8	chr22:29955000-29976000	Weak transcription	NHEK	skin
9	chr22:29955400-29976000	Weak transcription	HUVEC	blood vessel
10	chr22:29957400-29976200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr22:29957600-29976200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr22:29958000-29975800	Weak transcription	Stomach Mucosa	stomach
13	chr22:29958400-29976000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr22:29958400-29976200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:29958400-29976400	Weak transcription	Primary B cells from cord blood	blood
16	chr22:29958400-29976400	Weak transcription	NHDF-Ad	bronchial
17	chr22:29958600-29976200	Weak transcription	HSMM	muscle
18	chr22:29961000-29975800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr22:29961800-29974600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:29962200-29976000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr22:29963600-29976000	Weak transcription	Fetal Brain Male	brain
22	chr22:29963600-29976000	Weak transcription	NH-A	brain
23	chr22:29965200-29976000	Weak transcription	Fetal Kidney	kidney
24	chr22:29965200-29976400	Weak transcription	Fetal Lung	lung
25	chr22:29965400-29975800	Weak transcription	GM12878-XiMat	blood
26	chr22:29965400-29976000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr22:29965400-29976200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:29965400-29976200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:29965400-29976200	Weak transcription	Adipose Nuclei	Adipose
30	chr22:29965400-29976200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr22:29965400-29976200	Weak transcription	Colonic Mucosa	Colon
32	chr22:29965400-29976400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr22:29965400-29976400	Weak transcription	HSMMtube	muscle
34	chr22:29965600-29976200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr22:29965800-29976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr22:29965800-29976200	Weak transcription	Placenta	Placenta
37	chr22:29965800-29976400	Weak transcription	Brain Angular Gyrus	brain
38	chr22:29966000-29974400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr22:29966200-29975800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr22:29966200-29976200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr22:29966200-29976200	Weak transcription	Right Ventricle	heart
42	chr22:29966400-29974400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr22:29966400-29974600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr22:29966400-29975600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr22:29966400-29975600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr22:29966400-29976000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr22:29966400-29976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr22:29966400-29976000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr22:29966400-29976000	Weak transcription	NHLF	lung
50	chr22:29966400-29976200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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