Variant report

Variant	rs1025754
Chromosome Location	chr2:58336134-58336135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58327413..58329315-chr2:58335366..58337624,2	MCF-7	breast:
2	chr2:58328189..58330016-chr2:58335777..58337900,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10184957	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs12473245	0.87[ASN][1000 genomes]
rs12713377	0.81[CHD][hapmap]
rs13411119	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2110664	0.86[CHD][hapmap]
rs2118898	0.84[ASN][1000 genomes]
rs2165105	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732136	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6714952	0.84[JPT][hapmap]
rs6722988	0.81[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs7558066	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1025754	FANCL	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:58303000-58358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
4	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:58319400-58358400	Weak transcription	Ovary	ovary
7	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:58320000-58339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:58320000-58347600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
14	chr2:58322200-58347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:58322600-58349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:58322600-58350400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:58323200-58347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:58323200-58350400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:58323600-58350200	Weak transcription	Liver	Liver
20	chr2:58326400-58347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:58327000-58337600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:58327000-58339600	Weak transcription	K562	blood
23	chr2:58327000-58347600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:58332400-58370800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:58333000-58341800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:58334000-58336200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:58334400-58336400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:58334600-58336400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:58334600-58336800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:58334800-58336200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:58335200-58336200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:58335200-58339400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:58335200-58348200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:58335400-58336600	Enhancers	Hela-S3	cervix
35	chr2:58335400-58336800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:58335400-58336800	Flanking Active TSS	A549	lung
37	chr2:58335600-58336200	Enhancers	HMEC	breast
38	chr2:58335600-58336200	Enhancers	NHEK	skin
39	chr2:58335600-58336400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:58335600-58340000	Weak transcription	Stomach Mucosa	stomach
41	chr2:58335600-58347800	Weak transcription	Adipose Nuclei	Adipose
42	chr2:58335800-58336200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:58335800-58336400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:58335800-58336400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr2:58335800-58336400	Enhancers	NH-A	brain
46	chr2:58335800-58336600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:58335800-58336600	Enhancers	NHDF-Ad	bronchial
48	chr2:58335800-58336600	Enhancers	Osteobl	bone
49	chr2:58335800-58337000	Enhancers	NHLF	lung
50	chr2:58335800-58337200	Weak transcription	GM12878-XiMat	blood

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