Variant report

Variant	rs5998657
Chromosome Location	chr22:21962488-21962489
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:21960976..21962831-chr22:21982946..21984525,2	MCF-7	breast:
2	chr22:21960769..21962604-chr22:21970592..21972163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161179	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12160982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16984988	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17004026	1.00[EUR][1000 genomes]
rs2194827	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28436610	1.00[EUR][1000 genomes]
rs55771333	1.00[EUR][1000 genomes]
rs58384889	1.00[EUR][1000 genomes]
rs5994603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5994629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5998534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5998537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5998640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5998662	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5998690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5998733	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61757961	1.00[EUR][1000 genomes]
rs61763373	1.00[EUR][1000 genomes]
rs61763394	1.00[EUR][1000 genomes]
rs7289600	1.00[EUR][1000 genomes]
rs73384145	1.00[EUR][1000 genomes]
rs8139523	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914458	chr22:21747678-22070489	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
2	nsv482690	chr22:21807513-22016791	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
3	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers 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 miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
4	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
5	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
6	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
7	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
8	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 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	chr22:21937800-21965400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:21939600-21983200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr22:21943400-21963600	Strong transcription	Fetal Intestine Small	intestine
4	chr22:21946400-21980200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:21948800-21965200	Weak transcription	Fetal Kidney	kidney
6	chr22:21949200-21976600	Weak transcription	Fetal Brain Male	brain
7	chr22:21949400-21965400	Weak transcription	Hela-S3	cervix
8	chr22:21949600-21965200	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:21949800-21965200	Weak transcription	Brain Anterior Caudate	brain
10	chr22:21949800-21965400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr22:21949800-21965400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr22:21949800-21968800	Weak transcription	Stomach Mucosa	stomach
13	chr22:21950000-21965200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:21950000-21965200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:21950000-21965400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:21950000-21978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:21950200-21965200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr22:21950200-21965200	Weak transcription	NH-A	brain
19	chr22:21950200-21965400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr22:21950600-21964000	Weak transcription	HUVEC	blood vessel
21	chr22:21950600-21964400	Weak transcription	Fetal Brain Female	brain
22	chr22:21950600-21965200	Weak transcription	Fetal Lung	lung
23	chr22:21950600-21965400	Weak transcription	Aorta	Aorta
24	chr22:21950800-21963600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:21950800-21964400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:21951200-21964400	Weak transcription	NHLF	lung
27	chr22:21951200-21964600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr22:21951200-21964600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr22:21951200-21965000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr22:21951200-21965400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr22:21951400-21965200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr22:21951800-21964200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:21952000-21964200	Weak transcription	Osteobl	bone
34	chr22:21952800-21965400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr22:21953800-21964400	Weak transcription	Liver	Liver
36	chr22:21953800-21964400	Weak transcription	Brain Angular Gyrus	brain
37	chr22:21954000-21964000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr22:21954000-21965200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:21954000-21965400	Weak transcription	Brain Substantia Nigra	brain
40	chr22:21954200-21964400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr22:21954200-21964400	Weak transcription	NHDF-Ad	bronchial
42	chr22:21954400-21963800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr22:21957000-21964400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr22:21957000-21965200	Weak transcription	HSMM	muscle
45	chr22:21957000-21965400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:21957200-21963800	Weak transcription	Thymus	Thymus
47	chr22:21957200-21963800	Weak transcription	HepG2	liver
48	chr22:21957200-21964400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr22:21957200-21965400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr22:21957200-21965600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links