Variant report

Variant	rs7618618
Chromosome Location	chr3:45963497-45963498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45943266..45944977-chr3:45963147..45965893,2	MCF-7	breast:
2	chr3:45961740..45963512-chr3:45972118..45973716,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LZTFL1-1	chr3:45963121-45963934	predAs_ge08_CXCR6_1

Variant related genes	Relation type
ENSG00000201635	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1047444	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12330199	1.00[YRI][hapmap]
rs13315494	0.83[YRI][hapmap]
rs1488373	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1488374	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1532070	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2191030	0.88[CEU][hapmap]
rs6441934	0.82[CEU][hapmap]
rs6764244	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6805727	1.00[YRI][hapmap]
rs7130	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7634640	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9810934	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9825221	1.00[YRI][hapmap]
rs9860832	1.00[YRI][hapmap]
rs9875356	1.00[YRI][hapmap]
rs9880627	1.00[YRI][hapmap]

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
rs7618618	FYCO1	cis	Nerve Tibial	GTEx
rs7618618	FYCO1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
2	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
3	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
6	chr3:45957800-45969000	Weak transcription	K562	blood
7	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:45958000-45964400	Weak transcription	Stomach Mucosa	stomach
9	chr3:45958000-45964600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:45958000-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:45958000-45965000	Weak transcription	Osteobl	bone
12	chr3:45958000-45965200	Weak transcription	HSMM	muscle
13	chr3:45958000-45969000	Weak transcription	NH-A	brain
14	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
17	chr3:45958600-45968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:45958600-45970000	Weak transcription	Small Intestine	intestine
19	chr3:45958800-45964600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
23	chr3:45959000-45966000	Genic enhancers	Fetal Thymus	thymus
24	chr3:45959000-45973600	Weak transcription	Fetal Kidney	kidney
25	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:45959400-45965000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:45959400-45965200	Weak transcription	HMEC	breast
29	chr3:45959400-45965800	Genic enhancers	Thymus	Thymus
30	chr3:45959400-45965800	Genic enhancers	Dnd41	blood
31	chr3:45959400-45966000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:45959400-45971800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:45959400-45973400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:45959600-45965600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr3:45959600-45973200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:45959800-45965600	Weak transcription	Hela-S3	cervix
38	chr3:45959800-45974600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:45959800-45979800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:45959800-45979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:45960000-45965800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:45960000-45965800	Strong transcription	Adipose Nuclei	Adipose
44	chr3:45960000-45966000	Strong transcription	Liver	Liver
45	chr3:45960000-45966200	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:45960000-45967800	Strong transcription	Placenta	Placenta
47	chr3:45960000-45979400	Strong transcription	Fetal Intestine Large	intestine
48	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:45960200-45965200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:45960200-45965800	Strong transcription	Esophagus	oesophagus

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