Variant report

Variant	rs2085600
Chromosome Location	chr4:89779909-89779910
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	chr4:89778194..89779923-chr4:89788297..89790207,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10024506	1.00[YRI][hapmap]
rs10461165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1246642	0.83[CHD][hapmap]
rs12640274	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13149209	0.81[EUR][1000 genomes]
rs1379932	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1379933	0.93[ASN][1000 genomes]
rs1458551	0.82[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2446301	0.81[CHB][hapmap]
rs2464528	0.91[CHD][hapmap];0.84[JPT][hapmap]
rs2609255	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2609259	0.81[CHB][hapmap]
rs2609261	0.90[CHD][hapmap]
rs2609262	0.90[CHD][hapmap]
rs2609264	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs2609265	0.84[JPT][hapmap]
rs2704570	0.80[ASN][1000 genomes]
rs2869952	0.82[ASN][1000 genomes]
rs28767574	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904255	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4425336	0.81[EUR][1000 genomes]
rs56158219	0.91[ASN][1000 genomes]
rs57400569	0.81[EUR][1000 genomes]
rs6815970	0.81[ASN][1000 genomes]
rs6830970	0.82[CHD][hapmap]
rs7660000	0.87[GIH][hapmap]
rs9991039	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2085600	FAM13A	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89765000-89780400	Weak transcription	Ovary	ovary
2	chr4:89765000-89780600	Weak transcription	Left Ventricle	heart
3	chr4:89765200-89780400	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:89765400-89780400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:89765400-89780800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:89766000-89780400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:89767800-89780400	Weak transcription	Fetal Kidney	kidney
8	chr4:89767800-89780800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:89768800-89789400	Weak transcription	Fetal Intestine Small	intestine
10	chr4:89771000-89803200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:89773600-89784200	Weak transcription	Gastric	stomach
12	chr4:89775400-89780400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:89778400-89782800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr4:89778800-89780200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr4:89778800-89782200	Enhancers	Fetal Lung	lung
16	chr4:89779000-89781600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:89779400-89780800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:89779400-89781400	Enhancers	Primary hematopoietic stem cells	blood
19	chr4:89779600-89780000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr4:89779600-89780000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:89779600-89780000	Flanking Active TSS	GM12878-XiMat	blood
22	chr4:89779600-89780800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:89779600-89780800	Enhancers	NHDF-Ad	bronchial
24	chr4:89779600-89781000	Enhancers	Adipose Nuclei	Adipose
25	chr4:89779600-89781400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:89779600-89781600	Enhancers	Primary B cells from cord blood	blood
27	chr4:89779600-89782200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:89779800-89780000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:89779800-89780000	Enhancers	HSMMtube	muscle
30	chr4:89779800-89780200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:89779800-89780400	Enhancers	Placenta	Placenta
32	chr4:89779800-89780600	Enhancers	Primary B cells from peripheral blood	blood
33	chr4:89779800-89780800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:89779800-89781800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:89779800-89782400	Enhancers	Fetal Stomach	stomach

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