Variant report

Variant	rs7634640
Chromosome Location	chr3:45982119-45982120
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	POLR2A	chr3:45981876-45982286	K562	blood:	n/a	n/a
2	NFIC	chr3:45981856-45982367	ECC-1	luminal epithelium:	n/a	n/a
3	SETDB1	chr3:45982089-45982554	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:
2	chr3:45979673..45982315-chr3:46020948..46022553,2	K562	blood:

Variant related genes	Relation type
CXCR6	TF binding region
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1047444	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1488373	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1488374	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1532070	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2191030	0.89[CEU][hapmap]
rs2373088	0.80[EUR][1000 genomes]
rs6764244	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7130	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7618618	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9810934	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7634640	FYCO1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
2	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:45971800-45982400	Weak transcription	NHEK	skin
6	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
7	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
10	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
11	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
12	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:45977600-45983400	Weak transcription	Primary B cells from cord blood	blood
14	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:45978200-45982200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:45978400-45983800	Weak transcription	Spleen	Spleen
19	chr3:45978400-45986600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:45978800-45982800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:45979000-45987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:45979000-45988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
25	chr3:45979200-45987200	Weak transcription	Colonic Mucosa	Colon
26	chr3:45979200-45987800	Weak transcription	Brain Anterior Caudate	brain
27	chr3:45979200-45987800	Weak transcription	HepG2	liver
28	chr3:45979200-45988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:45979400-45982400	Weak transcription	Hela-S3	cervix
30	chr3:45979400-45983200	Weak transcription	Pancreas	Pancrea
31	chr3:45979600-45983200	Weak transcription	Esophagus	oesophagus
32	chr3:45979600-45984200	Weak transcription	Liver	Liver
33	chr3:45979800-45983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:45979800-45983600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:45979800-45983600	Weak transcription	Gastric	stomach
36	chr3:45980200-45982200	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr3:45980200-45982600	Genic enhancers	Dnd41	blood
38	chr3:45980200-45984800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:45980400-45982200	Enhancers	Fetal Heart	heart
40	chr3:45980400-45984800	Enhancers	Placenta	Placenta
41	chr3:45980600-45982400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:45980600-45984000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:45980800-45982400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:45980800-45983600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:45980800-45983600	Weak transcription	Adipose Nuclei	Adipose
46	chr3:45980800-45983800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:45980800-45984400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:45980800-45986800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:45980800-45988000	Weak transcription	NH-A	brain
50	chr3:45980800-45989200	Weak transcription	Fetal Brain Male	brain

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