Variant report

Variant	rs17099675
Chromosome Location	chr1:77335952-77335953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77335357..77338179-chr1:77371008..77373403,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1357330	1.00[ASW][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1403245	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1522623	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs1522624	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1522626	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1718924	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs74089796	1.00[AMR][1000 genomes]
rs74092203	1.00[AMR][1000 genomes]
rs74092206	0.92[AFR][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	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1005649	chr1:77141039-77398747	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1003386	chr1:77305197-77375536	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17099675	SYCE1	trans	lymphoblastoid	seeQTL
rs17099675	CCDC19	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77332800-77336000	Active TSS	Brain Angular Gyrus	brain
2	chr1:77332800-77336000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:77332800-77336200	Active TSS	Brain Cingulate Gyrus	brain
4	chr1:77332800-77336200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:77332800-77337400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:77333000-77336200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:77333000-77336400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:77335000-77336000	Enhancers	Fetal Brain Male	brain
9	chr1:77335000-77336800	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr1:77335000-77337400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:77335000-77337400	Active TSS	Brain Hippocampus Middle	brain
12	chr1:77335000-77337800	Weak transcription	Right Atrium	heart
13	chr1:77335000-77360000	Weak transcription	Ovary	ovary
14	chr1:77335000-77371000	Weak transcription	Aorta	Aorta
15	chr1:77335200-77336000	Active TSS	Brain Germinal Matrix	brain
16	chr1:77335200-77338400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:77335200-77341200	Weak transcription	Fetal Stomach	stomach
18	chr1:77335400-77336400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:77335600-77337000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:77335800-77336000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:77335800-77341000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:77335800-77341600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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