Variant report

Variant	rs532688
Chromosome Location	chr1:172149948-172149949
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	chr1:172146908..172150355-chr1:172151675..172155662,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10489298	0.81[JPT][hapmap]
rs10911299	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125882	0.94[JPT][hapmap]
rs16843944	0.81[JPT][hapmap]
rs1746427	0.81[JPT][hapmap]
rs473629	0.95[JPT][hapmap]
rs479960	0.95[JPT][hapmap]
rs484686	0.92[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs492746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs495590	0.82[CEU][hapmap]
rs508742	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs515060	0.81[JPT][hapmap]
rs537444	0.94[JPT][hapmap]
rs552191	0.81[JPT][hapmap]
rs555798	0.95[JPT][hapmap]
rs579989	0.95[JPT][hapmap]
rs583578	0.95[JPT][hapmap]
rs589209	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs598562	1.00[JPT][hapmap]
rs610587	0.81[JPT][hapmap]
rs633592	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs655853	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6689455	0.96[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs672740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs681398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs683128	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs687041	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][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	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs532688	C1orf112	cis	cerebellum	SCAN
rs532688	FMO1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172132800-172150000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:172145800-172150000	Weak transcription	Psoas Muscle	Psoas
3	chr1:172146600-172150200	Enhancers	Stomach Mucosa	stomach
4	chr1:172146800-172152000	Enhancers	Fetal Intestine Small	intestine
5	chr1:172147400-172154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:172147600-172151200	Enhancers	Fetal Intestine Large	intestine
7	chr1:172148800-172152000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr1:172149000-172150000	Enhancers	Primary T cells from cord blood	blood
9	chr1:172149000-172150000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:172149000-172150000	Enhancers	Brain Angular Gyrus	brain
11	chr1:172149000-172150000	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:172149000-172150000	Enhancers	Brain Substantia Nigra	brain
13	chr1:172149000-172150400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:172149000-172152800	Enhancers	Fetal Stomach	stomach
15	chr1:172149200-172150000	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:172149200-172150000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:172149200-172150000	Enhancers	Brain Anterior Caudate	brain
18	chr1:172149200-172150200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:172149200-172150600	Enhancers	Brain Hippocampus Middle	brain
20	chr1:172149400-172150000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:172149400-172150000	Enhancers	Fetal Lung	lung
22	chr1:172149400-172150000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:172149400-172150000	Flanking Active TSS	GM12878-XiMat	blood
24	chr1:172149400-172150000	Enhancers	HSMM	muscle
25	chr1:172149400-172150000	Enhancers	NHLF	lung
26	chr1:172149400-172150200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:172149400-172150200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:172149400-172150200	Weak transcription	Ovary	ovary
29	chr1:172149400-172150400	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:172149400-172150600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr1:172149400-172151000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:172149400-172151000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr1:172149400-172151600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:172149400-172152000	Enhancers	Fetal Heart	heart
35	chr1:172149600-172150000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:172149600-172150000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr1:172149600-172150000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:172149600-172150000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr1:172149600-172150200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:172149600-172150800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr1:172149600-172151400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:172149600-172153600	Weak transcription	Small Intestine	intestine
43	chr1:172149800-172150000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:172149800-172150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:172149800-172150000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:172149800-172150000	Enhancers	HUVEC	blood vessel
47	chr1:172149800-172150000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:172149800-172150000	Enhancers	NHEK	skin
49	chr1:172149800-172150200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:172149800-172150200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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