Variant report

Variant	rs397020
Chromosome Location	chr20:1205886-1205887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1205839-1206387	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1204614..1208313-chr20:1245857..1250887,4	K562	blood:

Variant related genes	Relation type
RAD21L1	TF binding region
ENSG00000101298	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs203537	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203538	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203542	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203543	0.94[ASN][1000 genomes]
rs203544	0.94[ASN][1000 genomes]
rs203545	0.94[ASN][1000 genomes]
rs203546	0.94[ASN][1000 genomes]
rs203547	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203548	0.94[ASN][1000 genomes]
rs203549	0.94[ASN][1000 genomes]
rs203550	0.94[ASN][1000 genomes]
rs203555	0.81[ASN][1000 genomes]
rs203556	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs396004	0.95[ASN][1000 genomes]
rs430731	0.98[ASN][1000 genomes]
rs446359	0.92[ASN][1000 genomes]
rs6078117	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
7	nsv516776	chr20:1195784-1233893	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv912586	chr20:1195784-1248286	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv518957	chr20:1195784-1250463	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3436470	chr20:1205377-1207925	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv3509885	chr20:1205427-1207700	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv3509887	chr20:1205427-1207700	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv912587	chr20:1205886-1248286	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	19010793	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs397020	RAD21L1	cis	parietal	SCAN
rs397020	SDCBP2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1204200-1206000	Weak transcription	Psoas Muscle	Psoas
2	chr20:1205600-1206000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr20:1205600-1206000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:1205600-1206000	Enhancers	Fetal Intestine Large	intestine
5	chr20:1205800-1206000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
6	chr20:1205800-1206000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
7	chr20:1205800-1206000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr20:1205800-1206000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr20:1205800-1206000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr20:1205800-1206000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr20:1205800-1206000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr20:1205800-1206000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr20:1205800-1206000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr20:1205800-1206000	Enhancers	Pancreas	Pancrea
15	chr20:1205800-1206000	Bivalent/Poised TSS	HepG2	liver
16	chr20:1205800-1206000	Flanking Active TSS	K562	blood
17	chr20:1205800-1206000	Active TSS	NHEK	skin
18	chr20:1205800-1206800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
19	chr20:1205800-1207000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr20:1205800-1207000	Active TSS	A549	lung
21	chr20:1205800-1207200	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr20:1205800-1207400	Active TSS	Primary T cells from cord blood	blood
23	chr20:1205800-1207600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr20:1205800-1207600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr20:1205800-1207800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr20:1205800-1207800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr20:1205800-1207800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr20:1205800-1207800	Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links