Variant report

Variant	rs713834
Chromosome Location	chr22:29440692-29440693
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29277889..29280481-chr22:29440283..29442464,3	MCF-7	breast:
2	chr22:29426264..29428504-chr22:29439113..29440872,2	K562	blood:
3	chr22:29195509..29198134-chr22:29437512..29441446,4	K562	blood:
4	chr22:29436800..29439536-chr22:29439547..29442052,2	K562	blood:
5	chr22:29440576..29442454-chr22:29442829..29445224,2	K562	blood:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000183579	Chromatin interaction
ENSG00000177993	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12484832	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12485244	0.88[EUR][1000 genomes]
rs132565	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17440734	0.96[CEU][hapmap]
rs1883197	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1977047	0.86[EUR][1000 genomes]
rs1983553	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064084	0.93[CEU][hapmap]
rs2072774	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2103544	0.89[EUR][1000 genomes]
rs2347789	0.82[EUR][1000 genomes]
rs2347790	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs28541979	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140643	0.96[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4333023	0.82[EUR][1000 genomes]
rs4404379	0.82[EUR][1000 genomes]
rs4580479	0.83[ASN][1000 genomes]
rs469994	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820794	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823002	1.00[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4823003	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4823005	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs5997430	0.91[EUR][1000 genomes]
rs5997431	0.89[EUR][1000 genomes]
rs5997432	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997433	0.93[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs5997434	0.93[EUR][1000 genomes]
rs5997435	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005954	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6005955	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6005956	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6005958	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6005959	0.89[EUR][1000 genomes]
rs6005964	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6005965	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6005967	1.00[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs727892	0.96[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7284304	0.89[EUR][1000 genomes]
rs7287517	0.89[EUR][1000 genomes]
rs7290304	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs738246	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8137254	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8137499	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8142591	0.88[EUR][1000 genomes]
rs874915	0.84[EUR][1000 genomes]
rs874916	0.88[EUR][1000 genomes]
rs874917	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608719	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9608721	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613771	0.81[EUR][1000 genomes]
rs9613776	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9613777	0.96[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs9613784	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613785	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs964589	1.00[CEU][hapmap];0.80[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs713834	SEZ6L	cis	cerebellum	SCAN
rs713834	GGT5	cis	parietal	SCAN
rs713834	DDT	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29427400-29448400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29427800-29451400	Weak transcription	Psoas Muscle	Psoas
3	chr22:29428000-29441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:29428600-29440800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr22:29428800-29443600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:29429000-29444000	Weak transcription	Right Ventricle	heart
7	chr22:29436400-29440800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr22:29436800-29441200	Genic enhancers	HepG2	liver
9	chr22:29436800-29442600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:29436800-29443800	Weak transcription	Hela-S3	cervix
11	chr22:29436800-29445600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr22:29437200-29441400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr22:29437200-29442200	Weak transcription	Small Intestine	intestine
14	chr22:29437200-29443000	Weak transcription	K562	blood
15	chr22:29437200-29443200	Weak transcription	Brain Angular Gyrus	brain
16	chr22:29437200-29443800	Weak transcription	Fetal Heart	heart
17	chr22:29437200-29450800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr22:29437600-29440800	Weak transcription	Adipose Nuclei	Adipose
19	chr22:29437800-29448800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr22:29437800-29450200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:29438000-29442000	Weak transcription	Brain Hippocampus Middle	brain
22	chr22:29438000-29442800	Weak transcription	Fetal Brain Male	brain
23	chr22:29438000-29447200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr22:29438200-29447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:29438400-29449800	Strong transcription	Fetal Stomach	stomach
26	chr22:29438400-29451800	Strong transcription	Fetal Intestine Small	intestine
27	chr22:29438600-29445400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr22:29438600-29445600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr22:29439000-29441400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr22:29439000-29447400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr22:29439000-29447400	Strong transcription	Fetal Intestine Large	intestine
32	chr22:29439000-29447400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr22:29439000-29449800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr22:29439000-29450200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr22:29439200-29440800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr22:29439200-29441000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr22:29439200-29441200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr22:29439200-29441400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:29439200-29445400	Strong transcription	Fetal Muscle Leg	muscle
40	chr22:29439200-29447000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr22:29439200-29447400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr22:29439200-29447400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr22:29439200-29447400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr22:29439200-29447400	Strong transcription	Pancreas	Pancrea
45	chr22:29439200-29447600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr22:29439200-29447600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:29439400-29441000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr22:29439400-29441000	Genic enhancers	NHEK	skin
49	chr22:29439400-29441200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr22:29439400-29447000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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