Variant report

Variant	rs1488374
Chromosome Location	chr3:45961842-45961843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:45961841-45962107	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:45960807-45962617	K562	blood:	n/a	n/a
3	REST	chr3:45961742-45962201	ECC-1	luminal epithelium:	n/a	n/a
4	REST	chr3:45961752-45962172	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45961740..45963512-chr3:45972118..45973716,2	MCF-7	breast:

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1047444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1488373	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1532070	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2191030	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2373088	0.81[EUR][1000 genomes]
rs6441934	1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6764244	0.95[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6806802	0.82[EUR][1000 genomes]
rs7130	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618618	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7634640	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7652331	0.86[MEX][hapmap]
rs9311379	0.84[EUR][1000 genomes]
rs9810934	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1488374	FYCO1	cis	lung	GTEx
rs1488374	FYCO1	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45949200-45962400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:45949800-45962600	Weak transcription	HepG2	liver
3	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
4	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
5	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:45957800-45962400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
15	chr3:45957800-45969000	Weak transcription	K562	blood
16	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:45958000-45962400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:45958000-45962800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:45958000-45964400	Weak transcription	Stomach Mucosa	stomach
20	chr3:45958000-45964600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:45958000-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:45958000-45965000	Weak transcription	Osteobl	bone
23	chr3:45958000-45965200	Weak transcription	HSMM	muscle
24	chr3:45958000-45969000	Weak transcription	NH-A	brain
25	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:45958200-45963200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:45958200-45963400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:45958400-45963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
31	chr3:45958600-45962000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:45958600-45963000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:45958600-45968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:45958600-45970000	Weak transcription	Small Intestine	intestine
35	chr3:45958800-45962600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:45958800-45964600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
40	chr3:45959000-45962800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:45959000-45966000	Genic enhancers	Fetal Thymus	thymus
42	chr3:45959000-45973600	Weak transcription	Fetal Kidney	kidney
43	chr3:45959200-45962200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:45959200-45962600	Weak transcription	NHEK	skin
45	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:45959400-45962000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:45959400-45962400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:45959400-45962800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:45959400-45962800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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