Variant report

Variant	rs3788423
Chromosome Location	chr22:30390990-30390991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30231401..30237558-chr22:30387473..30391733,6	MCF-7	breast:
2	chr22:30387371..30390104-chr22:30390840..30392967,2	MCF-7	breast:
3	chr22:30210116..30212715-chr22:30390306..30391990,2	MCF-7	breast:
4	chr22:30388182..30392809-chr22:30393222..30398050,6	K562	blood:
5	chr22:30388710..30391580-chr22:30397983..30401344,3	MCF-7	breast:
6	chr22:30388182..30391432-chr22:30393585..30396816,3	K562	blood:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10048885	0.82[AMR][1000 genomes]
rs1071888	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1076137	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs11090598	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12167333	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12168499	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12168552	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12171061	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12171250	0.82[EUR][1000 genomes]
rs12537	0.80[CEU][hapmap]
rs17643918	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17648725	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1807509	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193473	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs193481	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2017677	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051764	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105870	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2349225	0.91[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs2412960	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28257	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34862234	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35705048	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36578	0.88[JPT][hapmap];0.89[YRI][hapmap]
rs36580	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36586	0.82[AMR][1000 genomes]
rs36590	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36591	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36594	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36596	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36598	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36601	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36604	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36605	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36606	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36607	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3887275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3958025	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap]
rs39712	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41162	0.84[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41164	0.91[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs41166	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41172	0.83[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs41174	0.86[CEU][hapmap]
rs41175	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41179	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4239932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4239933	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4337577	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4823063	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4823070	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4993442	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5752968	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap]
rs5752986	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752988	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763630	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763634	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763644	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763680	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763691	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs715523	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718772	0.84[ASW][hapmap];0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7286070	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7292615	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737904	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737912	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7510705	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8135823	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8136147	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8139994	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8141404	0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8141680	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620926	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620943	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9620953	0.81[EUR][1000 genomes]
rs9625873	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9625874	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9625878	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625879	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9625919	0.95[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9625926	0.84[EUR][1000 genomes]
rs9625931	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3788423	TTC28	cis	cerebellum	SCAN
rs3788423	CRYBB3	cis	parietal	SCAN
rs3788423	KIAA1671	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
2	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
6	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr22:30376200-30394800	Weak transcription	GM12878-XiMat	blood
9	chr22:30377600-30402800	Weak transcription	Fetal Brain Male	brain
10	chr22:30378200-30398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:30378400-30391400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr22:30379200-30391200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr22:30380800-30391800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr22:30381000-30397600	Weak transcription	Fetal Kidney	kidney
15	chr22:30382600-30392000	Strong transcription	Primary T cells from cord blood	blood
16	chr22:30383800-30391600	Strong transcription	Primary B cells from cord blood	blood
17	chr22:30384200-30391000	Weak transcription	Brain Substantia Nigra	brain
18	chr22:30384200-30398400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:30384200-30403800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr22:30384400-30393400	Weak transcription	Brain Hippocampus Middle	brain
21	chr22:30384400-30404000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr22:30385000-30404000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr22:30386200-30402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr22:30386600-30391200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr22:30386800-30391000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr22:30387400-30391000	Strong transcription	Fetal Thymus	thymus
27	chr22:30387600-30391400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr22:30388000-30394400	Weak transcription	Lung	lung
29	chr22:30388000-30394600	Weak transcription	Fetal Lung	lung
30	chr22:30388000-30398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr22:30388200-30391800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:30388200-30392200	Enhancers	HMEC	breast
33	chr22:30388400-30391000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr22:30388400-30391800	Enhancers	NH-A	brain
35	chr22:30388400-30392200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr22:30388400-30392200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr22:30388600-30396800	Weak transcription	Brain Germinal Matrix	brain
38	chr22:30388600-30398200	Weak transcription	Spleen	Spleen
39	chr22:30388600-30400800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr22:30388800-30391600	Enhancers	Osteobl	bone
41	chr22:30388800-30391800	Enhancers	HSMM	muscle
42	chr22:30389000-30391000	Weak transcription	Brain Angular Gyrus	brain
43	chr22:30389000-30391600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr22:30389000-30398600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr22:30389200-30391200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr22:30389200-30391800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr22:30389200-30392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr22:30389200-30394800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr22:30389200-30398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr22:30389200-30402600	Weak transcription	Rectal Smooth Muscle	rectum

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