Variant report

Variant	rs438005
Chromosome Location	chr20:1207629-1207630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:109)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:109 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:1207500-1207650	NHDF-neo	bronchial:	n/a	n/a
2	MAX	chr20:1206410-1207808	A549	lung:	n/a	chr20:1207386-1207395
3	CTCF	chr20:1207507-1207644	Lung_OC	lung:	n/a	n/a
4	RAD21	chr20:1207459-1207632	HepG2	liver:	n/a	n/a
5	RAD21	chr20:1207511-1207666	HepG2	liver:	n/a	n/a
6	MAX	chr20:1206472-1207693	A549	lung:	n/a	chr20:1207386-1207395
7	CTCF	chr20:1207550-1207711	GM12891	blood:	n/a	n/a
8	CTCF	chr20:1207500-1207650	NHLF	lung:	n/a	n/a
9	JUND	chr20:1207533-1208178	K562	blood:	n/a	chr20:1207943-1207955
10	SP1	chr20:1207074-1207782	A549	lung:	n/a	chr20:1207150-1207164
11	CTCF	chr20:1207540-1207690	HepG2	liver:	n/a	n/a
12	CTCF	chr20:1207480-1207630	HPAF	blood vessel:	n/a	n/a
13	CTCF	chr20:1207480-1207630	GM06990	blood:	n/a	n/a
14	CTCF	chr20:1207484-1207690	HepG2	liver:	n/a	n/a
15	MAZ	chr20:1206086-1207723	K562	blood:	n/a	chr20:1207386-1207395
16	CTCF	chr20:1207515-1207717	ProgFib	skin:	n/a	n/a
17	CTCF	chr20:1207500-1207650	GM12873	blood:	n/a	n/a
18	RCOR1	chr20:1207264-1208141	K562	blood:	n/a	n/a
19	CTCF	chr20:1207436-1207733	K562	blood:	n/a	n/a
20	CTCF	chr20:1207518-1207677	GM13977	blood:	n/a	n/a
21	CTCF	chr20:1207531-1207649	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr20:1207500-1207650	HPF	lung:	n/a	n/a
23	CTCF	chr20:1207576-1207652	GM12892	blood:	n/a	n/a
24	CTCF	chr20:1207520-1207670	HCM	heart:	n/a	n/a
25	CTCF	chr20:1207516-1207658	GM10248	blood:	n/a	n/a
26	CTCF	chr20:1207480-1207630	AG04449	skin:	n/a	n/a
27	IRF1	chr20:1207385-1207703	K562	blood:	n/a	chr20:1207519-1207533 chr20:1207523-1207533
28	CTCF	chr20:1207460-1207684	K562	blood:	n/a	n/a
29	CTCF	chr20:1207480-1207630	Caco-2	colon:	n/a	n/a
30	CTCF	chr20:1207473-1207688	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr20:1207532-1207677	GM10266	blood:	n/a	n/a
32	CTCF	chr20:1207500-1207650	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr20:1207520-1207670	HVMF	connective:	n/a	n/a
34	CTCF	chr20:1207500-1207650	HCFaa	heart:	n/a	n/a
35	CTCF	chr20:1207560-1207710	HPF	lung:	n/a	n/a
36	CTCF	chr20:1207480-1207630	HCPEpiC	choroid plexus:	n/a	n/a
37	CTCF	chr20:1207511-1207683	GM19238	blood:	n/a	n/a
38	CTCF	chr20:1207504-1207666	MCF-7	breast:	n/a	n/a
39	CTCF	chr20:1207470-1207642	GM12878	blood:	n/a	n/a
40	CTCF	chr20:1207500-1207650	RPTEC	kidney:	n/a	n/a
41	CTCF	chr20:1207500-1207650	GM12867	blood:	n/a	n/a
42	CTCF	chr20:1207575-1207648	Pancreas_OC	pancreas:	n/a	n/a
43	CTCF	chr20:1207500-1207650	HepG2	liver:	n/a	n/a
44	CTCF	chr20:1207480-1207630	AG09309	skin:	n/a	n/a
45	CTCF	chr20:1207490-1207733	A549	lung:	n/a	n/a
46	CCNT2	chr20:1206635-1207632	K562	blood:	n/a	n/a
47	CTCF	chr20:1207480-1207630	GM12871	blood:	n/a	n/a
48	CTCF	chr20:1207500-1207650	HFF-Myc	foreskin:	n/a	n/a
49	CTCF	chr20:1207500-1207650	HCPEpiC	choroid plexus:	n/a	n/a
50	CTCF	chr20:1207453-1207774	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1206512..1208051-chr20:1245857..1247433,2	K562	blood:
2	chr20:1206586..1208814-chr20:1304748..1306483,2	K562	blood:
3	chr20:1206796..1208958-chr20:1209065..1211253,2	MCF-7	breast:
4	chr20:1207352..1209653-chr20:1227300..1229207,2	K562	blood:
5	chr20:1207162..1208733-chr20:1230513..1232075,2	K562	blood:
6	chr20:1206971..1208847-chr20:1236164..1237785,2	K562	blood:
7	chr20:1204614..1208313-chr20:1245857..1250887,4	K562	blood:
8	chr20:1206916..1209904-chr20:1219433..1221518,2	K562	blood:

No data

Variant related genes	Relation type
RAD21L1	TF binding region
ENSG00000244588	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000234684	Chromatin interaction
ENSG00000101298	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs62186522	0.92[EUR][1000 genomes]
rs62187482	0.92[EUR][1000 genomes]
rs62187484	0.92[EUR][1000 genomes]
rs62187492	0.84[EUR][1000 genomes]
rs62187493	0.84[EUR][1000 genomes]

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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1205800-1207800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr20:1205800-1207800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:1205800-1207800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr20:1205800-1207800	Active TSS	Brain Cingulate Gyrus	brain
5	chr20:1206000-1207800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:1206000-1207800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:1206000-1207800	Active TSS	Brain Anterior Caudate	brain
8	chr20:1206000-1207800	Active TSS	Psoas Muscle	Psoas
9	chr20:1206000-1207800	Bivalent/Poised TSS	NHEK	skin
10	chr20:1206000-1208000	Enhancers	Spleen	Spleen
11	chr20:1206000-1208000	Active TSS	K562	blood
12	chr20:1206800-1207800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr20:1206800-1207800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
14	chr20:1206800-1207800	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr20:1206800-1207800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr20:1206800-1207800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:1206800-1207800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr20:1206800-1207800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr20:1206800-1208000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr20:1206800-1208000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr20:1206800-1208200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
22	chr20:1206800-1208200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr20:1207000-1207800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr20:1207000-1207800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:1207000-1208000	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr20:1207000-1208200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr20:1207000-1208200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr20:1207000-1208200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr20:1207200-1207800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr20:1207200-1207800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:1207200-1207800	Active TSS	Lung	lung
32	chr20:1207200-1208000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
33	chr20:1207200-1208200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr20:1207400-1207800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr20:1207400-1207800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:1207400-1207800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:1207400-1207800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:1207400-1207800	Enhancers	Liver	Liver
39	chr20:1207400-1207800	Bivalent Enhancer	Colonic Mucosa	Colon
40	chr20:1207400-1207800	Enhancers	Duodenum Mucosa	Duodenum
41	chr20:1207400-1207800	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr20:1207400-1207800	Bivalent Enhancer	Fetal Stomach	stomach
43	chr20:1207400-1207800	Bivalent Enhancer	Fetal Thymus	thymus
44	chr20:1207400-1207800	Enhancers	Pancreas	Pancrea
45	chr20:1207400-1207800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr20:1207400-1208000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr20:1207400-1208000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr20:1207400-1208200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
49	chr20:1207400-1208200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
50	chr20:1207400-1208200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links