Variant report

Variant	rs13249929
Chromosome Location	chr8:10188617-10188618
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	chr8:9911693..9914058-chr8:10186837..10189075,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175806	Chromatin interaction
ENSG00000260093	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11990063	0.87[MKK][hapmap]
rs13250850	0.82[AMR][1000 genomes]
rs17151588	0.85[MEX][hapmap]
rs34113732	0.86[AMR][1000 genomes]
rs35130171	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4503102	0.85[MEX][hapmap];0.88[MKK][hapmap]
rs4577961	0.83[AMR][1000 genomes]
rs7837316	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9644722	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13249929	FAM167A	cis	parietal	SCAN
rs13249929	CTSB	cis	cerebellum	SCAN
rs13249929	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs13249929	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs13249929	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10176600-10191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:10178600-10190400	Weak transcription	Primary B cells from cord blood	blood
3	chr8:10179400-10189600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:10179400-10189800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr8:10179400-10190000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr8:10179400-10190000	Weak transcription	Brain Substantia Nigra	brain
7	chr8:10179400-10190400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr8:10179400-10190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:10179400-10191200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:10179400-10191200	Weak transcription	Fetal Intestine Small	intestine
11	chr8:10179400-10191200	Weak transcription	Pancreas	Pancrea
12	chr8:10179400-10192000	Weak transcription	Aorta	Aorta
13	chr8:10179600-10190200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr8:10180200-10190200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr8:10182600-10190600	Weak transcription	Spleen	Spleen
16	chr8:10182600-10192000	Weak transcription	Right Ventricle	heart
17	chr8:10183800-10188800	Weak transcription	Brain Germinal Matrix	brain
18	chr8:10184000-10189400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr8:10184000-10189600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr8:10184200-10189600	Weak transcription	GM12878-XiMat	blood
21	chr8:10184200-10190000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr8:10184400-10190000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:10184600-10189600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr8:10186000-10190800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:10186800-10189600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr8:10186800-10192200	Enhancers	Fetal Brain Male	brain
27	chr8:10187800-10190000	Enhancers	Primary T cells from cord blood	blood
28	chr8:10188000-10191200	Enhancers	Fetal Brain Female	brain
29	chr8:10188200-10189400	Enhancers	Brain Cingulate Gyrus	brain
30	chr8:10188400-10189400	Enhancers	Brain Anterior Caudate	brain
31	chr8:10188400-10190000	Weak transcription	Fetal Thymus	thymus
32	chr8:10188400-10190200	Enhancers	Brain Hippocampus Middle	brain
33	chr8:10188400-10190600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:10188600-10188800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr8:10188600-10188800	Enhancers	Brain Angular Gyrus	brain
36	chr8:10188600-10189000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:10188600-10189000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr8:10188600-10189200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr8:10188600-10189200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr8:10188600-10190200	Enhancers	Brain Inferior Temporal Lobe	brain

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