Variant report

Variant	rs3753305
Chromosome Location	chr1:169554058-169554059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169553531..169554398-chr1:169563651..169564307,2	MCF-7	breast:
2	chr1:169554006..169554804-chrX:81997894..81998531,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10753787	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800457	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894697	0.90[ASN][1000 genomes]
rs1894698	0.90[ASN][1000 genomes]
rs1894699	0.90[ASN][1000 genomes]
rs1981491	0.90[ASN][1000 genomes]
rs2187955	0.93[ASN][1000 genomes]
rs2205896	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2239853	0.90[ASN][1000 genomes]
rs3917782	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3917783	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3917786	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656188	0.90[ASN][1000 genomes]
rs4656688	0.90[ASN][1000 genomes]
rs4656689	0.90[ASN][1000 genomes]
rs6127	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6427202	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670678	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678795	0.93[ASN][1000 genomes]
rs6685578	0.93[ASN][1000 genomes]
rs7540556	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548857	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv548187	chr1:169530837-169559035	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv872534	chr1:169533266-169561274	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3753305	ZDHHC14	trans	cerebellum	SCAN
rs3753305	C11orf71	trans	cerebellum	SCAN
rs3753305	FMO9P	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169542200-169554800	Weak transcription	Placenta	Placenta
2	chr1:169543800-169554200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169553600-169554400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:169553600-169554400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:169553600-169554400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:169553600-169554400	Enhancers	NHEK	skin
7	chr1:169553800-169554200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:169553800-169554200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:169553800-169554400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:169553800-169554400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:169553800-169554400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:169553800-169554400	Enhancers	Primary T cells from cord blood	blood
13	chr1:169553800-169554400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:169553800-169554400	Enhancers	HMEC	breast
15	chr1:169553800-169554800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:169553800-169555200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:169553800-169555400	Active TSS	Primary T cells fromperipheralblood	blood
18	chr1:169553800-169555800	Active TSS	Liver	Liver
19	chr1:169554000-169554200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:169554000-169554200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:169554000-169554200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
22	chr1:169554000-169554200	Flanking Active TSS	Right Atrium	heart
23	chr1:169554000-169554400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:169554000-169554400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr1:169554000-169554400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:169554000-169554400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:169554000-169554400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:169554000-169554400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr1:169554000-169554400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:169554000-169554400	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
31	chr1:169554000-169555000	Active TSS	HepG2	liver
32	chr1:169554000-169555600	Bivalent/Poised TSS	Primary B cells from cord blood	blood

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