Variant report

Variant	rs2064084
Chromosome Location	chr22:29412257-29412258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29401603..29404388-chr22:29410754..29413254,2	K562	blood:
2	chr22:29411148..29412690-chr22:29641061..29643076,2	K562	blood:
3	chr22:29411681..29414398-chr22:29425375..29427146,2	K562	blood:
4	chr22:29262470..29264565-chr22:29409487..29412264,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12484832	0.91[CEU][hapmap]
rs12485244	0.95[ASN][1000 genomes]
rs132565	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17440734	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1977047	0.97[ASN][1000 genomes]
rs1983553	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs2072774	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2103544	0.96[ASN][1000 genomes]
rs2347789	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347790	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140643	0.96[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4333023	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4404379	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4594553	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4616575	0.96[ASN][1000 genomes]
rs469994	0.96[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4820794	0.96[CEU][hapmap]
rs4823002	0.93[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823003	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4823005	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5762942	0.84[MKK][hapmap]
rs5997430	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997431	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997432	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5997433	1.00[CEU][hapmap]
rs5997434	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005954	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6005955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005959	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005964	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005965	0.96[CEU][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6005967	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs713834	0.93[CEU][hapmap]
rs727892	0.96[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap]
rs7284304	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7287517	0.94[ASN][1000 genomes]
rs7290304	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs738246	0.92[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs8137254	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs8137499	0.96[CEU][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8142591	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs874915	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs874916	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874917	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9608719	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs9613768	0.89[CHD][hapmap]
rs9613771	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613776	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9613777	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613782	0.87[CHD][hapmap]
rs9613785	0.93[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs964589	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2064084	GGT5	cis	parietal	SCAN
rs2064084	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29400600-29425400	Weak transcription	NHEK	skin
2	chr22:29401200-29413400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29401400-29414800	Weak transcription	Esophagus	oesophagus
4	chr22:29401400-29419200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr22:29401400-29425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr22:29401800-29426200	Weak transcription	Colon Smooth Muscle	Colon
7	chr22:29405200-29418000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr22:29405400-29424600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:29407800-29413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:29408200-29419400	Weak transcription	Fetal Stomach	stomach
11	chr22:29408200-29419400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr22:29408200-29422600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr22:29408600-29419400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr22:29408600-29419400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr22:29409200-29414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:29409400-29414800	Weak transcription	Aorta	Aorta
17	chr22:29409600-29413800	Weak transcription	Fetal Lung	lung
18	chr22:29409800-29412600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr22:29410400-29416000	Enhancers	Liver	Liver
20	chr22:29410400-29419200	Weak transcription	Right Atrium	heart
21	chr22:29410400-29424800	Weak transcription	Psoas Muscle	Psoas
22	chr22:29410600-29412400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr22:29410800-29412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr22:29410800-29412400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr22:29410800-29418000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr22:29411000-29412400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr22:29411000-29414800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:29411000-29414800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:29411000-29417800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr22:29411000-29418400	Weak transcription	Right Ventricle	heart
31	chr22:29411000-29418800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr22:29411000-29419200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr22:29411000-29419400	Weak transcription	Left Ventricle	heart
34	chr22:29411000-29422200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr22:29411400-29412400	Enhancers	HepG2	liver
36	chr22:29411600-29414800	Enhancers	Fetal Intestine Small	intestine
37	chr22:29411800-29412600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr22:29411800-29412600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr22:29411800-29413000	Enhancers	Primary T cells from cord blood	blood
40	chr22:29411800-29414000	Enhancers	Duodenum Mucosa	Duodenum
41	chr22:29412000-29412400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr22:29412000-29412600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr22:29412000-29412600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr22:29412000-29413000	Enhancers	Brain Anterior Caudate	brain
45	chr22:29412000-29413000	Enhancers	A549	lung
46	chr22:29412000-29413800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:29412000-29413800	Enhancers	Pancreas	Pancrea
48	chr22:29412000-29414400	Enhancers	Fetal Kidney	kidney
49	chr22:29412000-29415000	Enhancers	Fetal Intestine Large	intestine
50	chr22:29412200-29412400	Enhancers	Brain Germinal Matrix	brain

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