Variant report

Variant	rs5998473
Chromosome Location	chr22:32791508-32791509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:32096851-32100847..22:32787968-32792766	K562	blood:
2	22:32477762-32487457..22:32787968-32792766	Hela-S3	cervix:
3	chr22:32791211..32793913-chr22:32796034..32798432,2	MCF-7	breast:
4	22:31864703-31891033..22:32787968-32792766	K562	blood:
5	22:32264718-32278135..22:32787968-32792766	GM12878	blood:
6	22:32170492-32188129..22:32787968-32792766	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000198089	Chromatin interaction
ENSG00000199248	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000100170	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000183530	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1009401	1.00[CHB][hapmap]
rs11545749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703546	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[ASN][1000 genomes]
rs12167726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16990408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16990443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs16990445	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs28783498	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35856742	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55807703	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028423	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034165	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998418	1.00[ASN][1000 genomes]
rs5998424	1.00[ASN][1000 genomes]
rs61095402	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67688485	0.86[EUR][1000 genomes]
rs67737467	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67967684	0.91[EUR][1000 genomes]
rs68016118	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68023238	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68125825	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166344	1.00[ASN][1000 genomes]
rs73166353	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166400	1.00[EUR][1000 genomes]
rs73168708	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168732	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170304	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170321	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170333	0.80[EUR][1000 genomes]
rs9619261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9621435	1.00[ASW][hapmap];0.82[CEU][hapmap];0.86[MEX][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32777200-32793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr22:32780800-32806400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:32781200-32793600	Strong transcription	Fetal Kidney	kidney
5	chr22:32781200-32798200	Strong transcription	Thymus	Thymus
6	chr22:32781200-32799200	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr22:32781200-32801200	Strong transcription	Fetal Stomach	stomach
8	chr22:32781200-32802200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr22:32781200-32803200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
17	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr22:32781400-32793000	Strong transcription	Fetal Intestine Small	intestine
19	chr22:32781400-32798200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:32781400-32798200	Strong transcription	Brain Anterior Caudate	brain
21	chr22:32781400-32798200	Strong transcription	NH-A	brain
22	chr22:32781400-32799200	Strong transcription	Lung	lung
23	chr22:32781400-32801200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr22:32781400-32802600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr22:32781400-32802600	Strong transcription	GM12878-XiMat	blood
26	chr22:32781400-32802600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr22:32781400-32803200	Strong transcription	Adipose Nuclei	Adipose
28	chr22:32781400-32803200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr22:32781400-32803600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr22:32781400-32803800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr22:32781400-32803800	Strong transcription	Liver	Liver
32	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
34	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr22:32781400-32804600	Strong transcription	Dnd41	blood
36	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:32781400-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr22:32781400-32805000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr22:32781400-32805000	Strong transcription	Fetal Intestine Large	intestine
45	chr22:32781400-32805000	Strong transcription	Fetal Lung	lung
46	chr22:32781400-32805000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr22:32781400-32805000	Strong transcription	Left Ventricle	heart
48	chr22:32781400-32805000	Strong transcription	Osteobl	bone
49	chr22:32781400-32805200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr22:32781400-32805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links