Variant report

Variant	rs5762916
Chromosome Location	chr22:29358219-29358220
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	chr22:29357505..29361534-chr22:29364431..29368155,3	K562	blood:
2	chr22:29279602..29282163-chr22:29357166..29358723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs132530	1.00[JPT][hapmap]
rs132541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs132547	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs132550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs132551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs132554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs132556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16986909	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs469988	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs5752844	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762924	0.87[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap]
rs5762935	0.87[CEU][hapmap];0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs713892	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs739197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5762916	RP3-366L4.2	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29348200-29365000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr22:29348800-29360400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr22:29349200-29365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29349200-29371800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:29349200-29371800	Weak transcription	HSMM	muscle
6	chr22:29349600-29359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:29349800-29360400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr22:29350000-29358400	Weak transcription	Fetal Lung	lung
9	chr22:29350000-29363000	Weak transcription	Liver	Liver
10	chr22:29350000-29372800	Weak transcription	Aorta	Aorta
11	chr22:29350400-29361000	Weak transcription	Ovary	ovary
12	chr22:29351400-29362200	Genic enhancers	HepG2	liver
13	chr22:29352400-29359600	Weak transcription	Gastric	stomach
14	chr22:29352800-29360400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr22:29353000-29359200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr22:29353200-29358400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr22:29353400-29358400	Weak transcription	Brain Angular Gyrus	brain
18	chr22:29354800-29360600	Weak transcription	Right Ventricle	heart
19	chr22:29354800-29364800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:29354800-29365600	Weak transcription	Lung	lung
21	chr22:29355200-29365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr22:29355400-29358400	Weak transcription	Left Ventricle	heart
23	chr22:29355400-29360400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr22:29355400-29360800	Weak transcription	Colon Smooth Muscle	Colon
25	chr22:29355400-29363600	Weak transcription	Fetal Stomach	stomach
26	chr22:29355400-29364800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr22:29355400-29365000	Weak transcription	Right Atrium	heart
28	chr22:29355400-29365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr22:29355400-29372800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr22:29355800-29364600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr22:29356000-29359000	Weak transcription	Pancreas	Pancrea
32	chr22:29356000-29360400	Weak transcription	Esophagus	oesophagus
33	chr22:29356000-29365400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr22:29356800-29358800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr22:29356800-29366400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:29357000-29358600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr22:29357000-29359400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr22:29357200-29359400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr22:29357200-29360400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr22:29357400-29358400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr22:29357400-29358800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr22:29357400-29359000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr22:29357400-29359600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr22:29357400-29360000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr22:29357400-29360600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:29357600-29359200	Enhancers	Brain Substantia Nigra	brain
47	chr22:29357600-29360200	Enhancers	Brain Anterior Caudate	brain
48	chr22:29357600-29360600	Weak transcription	Psoas Muscle	Psoas
49	chr22:29357600-29364800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr22:29357800-29358400	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links