Variant report

Variant	rs9289975
Chromosome Location	chr3:156783597-156783598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156778985..156781470-chr3:156781540..156783699,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10513500	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10513501	1.00[CEU][hapmap]
rs10513502	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1482850	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1482861	0.82[CEU][hapmap]
rs1482862	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16826968	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17443114	0.82[CEU][hapmap]
rs17449793	0.82[EUR][1000 genomes]
rs17450413	0.88[EUR][1000 genomes]
rs2321456	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs28436625	0.90[AFR][1000 genomes]
rs57283824	0.82[ASN][1000 genomes]
rs57791022	0.88[EUR][1000 genomes]
rs59981665	0.88[EUR][1000 genomes]
rs73873771	0.86[EUR][1000 genomes]
rs73873782	0.82[ASN][1000 genomes]
rs9990369	0.89[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9289975	RAI14	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156780800-156784200	Enhancers	Brain Substantia Nigra	brain
2	chr3:156780800-156785200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:156781000-156784200	Enhancers	Brain Anterior Caudate	brain
4	chr3:156781200-156784200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr3:156781200-156785400	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:156781400-156784600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr3:156781400-156785200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:156781600-156784000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
9	chr3:156781600-156785400	Enhancers	Brain Angular Gyrus	brain
10	chr3:156781600-156785800	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:156781800-156784000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:156782000-156783600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr3:156782000-156784000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr3:156782000-156787200	Enhancers	Fetal Thymus	thymus
15	chr3:156782200-156783600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:156782200-156783800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:156782200-156784200	Weak transcription	NH-A	brain
18	chr3:156782200-156784600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:156782400-156783600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:156782400-156783800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:156782400-156783800	Weak transcription	Fetal Brain Male	brain
22	chr3:156782400-156784000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:156782400-156784200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:156782400-156784400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:156782400-156787600	Weak transcription	Stomach Mucosa	stomach
26	chr3:156782400-156794000	Weak transcription	Right Atrium	heart
27	chr3:156782600-156783600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:156782600-156784600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:156782600-156784600	Weak transcription	Fetal Brain Female	brain
30	chr3:156782600-156784600	Weak transcription	K562	blood
31	chr3:156782600-156784800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:156782600-156795000	Weak transcription	Fetal Heart	heart
33	chr3:156782800-156783800	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr3:156782800-156784200	Weak transcription	Brain Germinal Matrix	brain
35	chr3:156782800-156784400	Weak transcription	Primary B cells from cord blood	blood
36	chr3:156782800-156784600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
37	chr3:156782800-156787600	Weak transcription	Fetal Intestine Large	intestine
38	chr3:156782800-156789400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:156782800-156795000	Weak transcription	Adipose Nuclei	Adipose
40	chr3:156783000-156783600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:156783000-156783600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:156783000-156786400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:156783200-156783600	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:156783200-156784000	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:156783200-156784200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr3:156783200-156785800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:156783200-156785800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:156783200-156786600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:156783200-156786600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:156783200-156786800	Enhancers	Primary T cells fromperipheralblood	blood

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