Variant report

Variant	rs521428
Chromosome Location	chr1:93445497-93445498
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	chr1:93331313..93333076-chr1:93443044..93445998,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1011663	0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs10874752	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164827	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs11164838	0.88[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs11164848	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164849	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164850	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs11164851	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs11164854	0.87[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11164855	0.80[GIH][hapmap]
rs12049007	0.90[ASN][1000 genomes]
rs12092304	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12120036	0.90[ASN][1000 genomes]
rs12130044	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs12144226	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12747275	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1678784	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2086314	0.90[ASN][1000 genomes]
rs2127398	0.90[ASN][1000 genomes]
rs2127400	0.90[ASN][1000 genomes]
rs3943283	0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4515797	0.81[ASN][1000 genomes]
rs4847226	0.89[ASN][1000 genomes]
rs4847386	0.83[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847389	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs534409	0.81[ASN][1000 genomes]
rs567613	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579800	0.80[EUR][1000 genomes]
rs594527	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606344	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs619784	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660870	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs663112	0.88[ASN][1000 genomes]
rs6671078	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6671268	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681240	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6681345	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7517539	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7524934	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs753391	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs770883	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs770884	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs521428	FAM69A	cis	Artery Tibial	GTEx
rs521428	CDC73	trans	cerebellum	SCAN
rs521428	BARHL2	cis	parietal	SCAN
rs521428	MTF2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:93434200-93445600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:93438800-93446000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:93439400-93446400	Weak transcription	Thymus	Thymus
5	chr1:93439600-93445600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:93439600-93446000	Weak transcription	Fetal Thymus	thymus
7	chr1:93439600-93446400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:93441000-93447800	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:93441600-93445600	Weak transcription	Primary T cells from cord blood	blood
10	chr1:93441600-93445600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:93441600-93446000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:93441600-93446200	Weak transcription	Dnd41	blood
13	chr1:93441800-93445800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:93442200-93445800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:93442800-93448400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:93443400-93445600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:93443400-93446000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:93444200-93446200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr1:93444200-93448800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:93445000-93445600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:93445200-93446200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:93445400-93445600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:93445400-93445600	Flanking Active TSS	GM12878-XiMat	blood
24	chr1:93445400-93446400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:93445400-93448000	Enhancers	Primary B cells from cord blood	blood
26	chr1:93445400-93448800	Enhancers	Primary T helper cells fromperipheralblood	blood

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