Variant report

Variant	rs2267278
Chromosome Location	chr22:34130913-34130914
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1001213	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12157940	0.80[JPT][hapmap]
rs16992908	0.87[CHB][hapmap]
rs16992910	0.81[CHB][hapmap]
rs16992923	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs16992929	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs16992967	0.88[CHD][hapmap]
rs2267276	0.81[JPT][hapmap]
rs2267277	0.93[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2267279	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267280	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267281	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283934	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2283935	0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2283936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283937	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283938	0.93[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs5999080	0.88[ASN][1000 genomes]
rs5999081	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs5999082	0.81[CHB][hapmap]
rs5999084	0.90[CHD][hapmap]
rs5999085	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5999086	0.81[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs5999087	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs5999088	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62225407	0.85[ASN][1000 genomes]
rs9619373	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1055203	chr22:34098417-34196685	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv459878	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv588936	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1060684	chr22:34108462-34140653	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv524432	chr22:34119866-34146368	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv522709	chr22:34124976-34131153	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2267278	TIMP3	cis	cerebellum	SCAN
rs2267278	CABP7	cis	parietal	SCAN
rs2267278	APOL5	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34105600-34133400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:34111200-34146200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr22:34111800-34142800	Weak transcription	Fetal Intestine Small	intestine
4	chr22:34116400-34135800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:34120200-34135600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:34120400-34135800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:34121600-34136800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr22:34123200-34152000	Weak transcription	Aorta	Aorta
9	chr22:34123800-34140800	Weak transcription	Fetal Stomach	stomach
10	chr22:34124800-34133000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:34124800-34171000	Weak transcription	Ovary	ovary
12	chr22:34126000-34133000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:34126000-34135400	Weak transcription	Right Ventricle	heart
14	chr22:34126000-34137600	Weak transcription	Psoas Muscle	Psoas
15	chr22:34126200-34132000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
17	chr22:34128200-34133200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr22:34128600-34143200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr22:34129000-34132000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr22:34129000-34134400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:34129200-34133600	Weak transcription	Left Ventricle	heart
22	chr22:34129400-34131000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr22:34129600-34131200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr22:34130000-34131200	Enhancers	Brain Substantia Nigra	brain
25	chr22:34130200-34133200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:34130400-34131000	Enhancers	Brain Cingulate Gyrus	brain
27	chr22:34130400-34131000	Enhancers	Brain Hippocampus Middle	brain
28	chr22:34130400-34133800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:34130400-34133800	Weak transcription	Fetal Heart	heart
30	chr22:34130600-34132000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr22:34130600-34133400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:34130800-34131200	Enhancers	Brain Anterior Caudate	brain
33	chr22:34130800-34131800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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