Variant report

Variant	rs241716
Chromosome Location	chr22:33383799-33383800
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	chr22:33382445..33385028-chr22:33386160..33388841,3	MCF-7	breast:
2	chr22:33379303..33380936-chr22:33382275..33384664,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs133940	0.89[CHB][hapmap]
rs133953	0.89[CHB][hapmap]
rs133955	0.89[CHB][hapmap]
rs241710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs241713	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241720	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241723	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs241730	0.86[EUR][1000 genomes]
rs241734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs241735	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs470009	0.89[CHB][hapmap]
rs470012	0.89[CHB][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	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs241716	GATSL3	cis	parietal	SCAN
rs241716	XBP1	cis	cerebellum	SCAN
rs241716	SF3A1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33354600-33387400	Weak transcription	Fetal Brain Female	brain
2	chr22:33380400-33384000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:33380800-33389200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr22:33381000-33383800	Enhancers	Fetal Stomach	stomach
5	chr22:33381000-33385400	Enhancers	NHEK	skin
6	chr22:33381200-33383800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr22:33381400-33385200	Enhancers	Fetal Muscle Leg	muscle
8	chr22:33381400-33385400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr22:33381600-33383800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr22:33381600-33384000	Enhancers	Placenta	Placenta
11	chr22:33381800-33383800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:33381800-33383800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:33381800-33383800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr22:33381800-33383800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr22:33381800-33383800	Enhancers	Brain Germinal Matrix	brain
16	chr22:33381800-33383800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr22:33381800-33384000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr22:33381800-33385000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr22:33381800-33386600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr22:33381800-33389200	Enhancers	HMEC	breast
21	chr22:33382000-33383800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr22:33382000-33383800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr22:33382000-33383800	Enhancers	HSMMtube	muscle
24	chr22:33382000-33384000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr22:33382000-33390200	Weak transcription	Right Atrium	heart
26	chr22:33382200-33383800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr22:33382200-33384000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr22:33382200-33384000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr22:33382400-33383800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr22:33382400-33383800	Enhancers	Brain Cingulate Gyrus	brain
31	chr22:33382400-33384000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr22:33382400-33384800	Weak transcription	Esophagus	oesophagus
33	chr22:33382400-33387600	Weak transcription	NHDF-Ad	bronchial
34	chr22:33382400-33392400	Weak transcription	Lung	lung
35	chr22:33382400-33404200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:33382600-33384600	Weak transcription	Spleen	Spleen
37	chr22:33382600-33387600	Weak transcription	Brain Angular Gyrus	brain
38	chr22:33382600-33387800	Weak transcription	Brain Substantia Nigra	brain
39	chr22:33382600-33387800	Weak transcription	Colon Smooth Muscle	Colon
40	chr22:33382600-33390400	Weak transcription	Right Ventricle	heart
41	chr22:33383200-33387600	Weak transcription	Fetal Heart	heart
42	chr22:33383400-33383800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr22:33383400-33383800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr22:33383400-33387400	Weak transcription	Adipose Nuclei	Adipose
45	chr22:33383400-33387400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr22:33383600-33384600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr22:33383600-33384600	Weak transcription	Hela-S3	cervix
48	chr22:33383600-33384800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr22:33383600-33386800	Weak transcription	Left Ventricle	heart
50	chr22:33383600-33387400	Weak transcription	Fetal Brain Male	brain

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