Variant report

Variant	rs2071574
Chromosome Location	chr19:55686138-55686139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr19:55685898-55686782	K562	blood:	n/a	n/a
2	E2F6	chr19:55685800-55686165	K562	blood:	n/a	n/a
3	E2F6	chr19:55684835-55686266	A549	lung:	n/a	chr19:55685236-55685247 chr19:55685240-55685247 chr19:55685060-55685072
4	NR2F2	chr19:55685557-55686138	K562	blood:	n/a	n/a
5	POLR2A	chr19:55685563-55686879	K562	blood:	n/a	n/a
6	TBP	chr19:55685103-55686800	K562	blood:	n/a	n/a
7	RCOR1	chr19:55685301-55686528	K562	blood:	n/a	n/a
8	PML	chr19:55685067-55686889	K562	blood:	n/a	n/a
9	E2F6	chr19:55685724-55686209	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZC3H11A	chr19:55685931-55686651	K562	blood:	n/a	n/a
11	MXI1	chr19:55685991-55686175	K562	blood:	n/a	n/a
12	POLR2A	chr19:55684921-55686855	K562	blood:	n/a	n/a
13	CBX3	chr19:55685731-55686234	K562	blood:	n/a	n/a
14	HEY1	chr19:55685614-55686357	K562	blood:	n/a	n/a
15	MAX	chr19:55685820-55686143	K562	blood:	n/a	n/a
16	HMGN3	chr19:55686013-55686153	K562	blood:	n/a	n/a
17	TAF7	chr19:55685914-55686374	K562	blood:	n/a	n/a
18	POLR2A	chr19:55684256-55687473	K562	blood:	n/a	n/a
19	POLR2A	chr19:55685838-55686769	H1-neurons	neurons:	n/a	n/a
20	GTF2B	chr19:55686009-55686875	K562	blood:	n/a	n/a
21	POLR2A	chr19:55684725-55687295	K562	blood:	n/a	n/a
22	MAX	chr19:55685799-55686214	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:55685062-55686816	K562	blood:	n/a	n/a
24	MAX	chr19:55684650-55686257	A549	lung:	n/a	n/a
25	JUN	chr19:55684455-55688134	K562	blood:	n/a	chr19:55686466-55686475 chr19:55687873-55687887 chr19:55685270-55685279
26	POLR2A	chr19:55685070-55686963	K562	blood:	n/a	n/a
27	E2F6	chr19:55685634-55686994	H1-hESC	embryonic stem cell:	n/a	chr19:55686468-55686477
28	E2F6	chr19:55685790-55686315	K562	blood:	n/a	n/a
29	TEAD4	chr19:55685105-55686910	K562	blood:	n/a	n/a
30	ZMIZ1	chr19:55686056-55686245	K562	blood:	n/a	n/a
31	EGR1	chr19:55686112-55686606	K562	blood:	n/a	chr19:55686528-55686537 chr19:55686486-55686496
32	POLR2A	chr19:55685890-55686864	K562	blood:	n/a	n/a
33	POLR2A	chr19:55685402-55688569	H1-neurons	neurons:	n/a	n/a
34	E2F6	chr19:55685609-55687141	K562	blood:	n/a	chr19:55686468-55686477
35	MAX	chr19:55685799-55687151	K562	blood:	n/a	n/a
36	POLR2A	chr19:55685601-55686387	K562	blood:	n/a	n/a
37	POLR2A	chr19:55684911-55687042	K562	blood:	n/a	n/a
38	POLR2A	chr19:55684974-55686834	K562	blood:	n/a	n/a
39	TAF7	chr19:55686085-55686281	K562	blood:	n/a	n/a
40	ELF1	chr19:55684954-55686161	K562	blood:	n/a	n/a
41	HEY1	chr19:55685504-55686892	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55683524..55688236-chr19:55723837..55729899,9	K562	blood:
2	chr19:55684227..55686502-chr19:56163659..56165514,2	K562	blood:
3	chr19:55685207..55686933-chr19:55998048..56001042,3	K562	blood:
4	chr19:55684986..55687245-chr19:55917365..55919407,3	K562	blood:
5	chr19:55685793..55687332-chr19:56110126..56112536,2	K562	blood:
6	chr19:55652583..55654587-chr19:55685564..55687103,2	K562	blood:
7	chr19:55677803..55679380-chr19:55684043..55686956,2	MCF-7	breast:
8	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
9	chr19:55651262..55654083-chr19:55684163..55687103,3	K562	blood:
10	chr19:55682890..55686413-chr19:55726859..55729575,3	K562	blood:
11	chr19:55684707..55688022-chr19:55908129..55911789,4	K562	blood:
12	chr19:55590426..55594638-chr19:55684228..55687886,4	K562	blood:
13	chr19:55685149..55688070-chr19:55790255..55792658,4	K562	blood:
14	chr19:55624933..55628932-chr19:55685116..55688802,5	K562	blood:
15	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
16	chr19:55592011..55594638-chr19:55684282..55687431,3	K562	blood:
17	chr19:55685793..55687548-chr19:56110126..56112399,2	K562	blood:
18	chr19:55684986..55687548-chr19:55917710..55920086,4	K562	blood:
19	chr19:55627139..55630124-chr19:55683805..55687284,3	K562	blood:

No data

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000133265	Chromatin interaction
ENSG00000179954	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000063244	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10423713	0.80[ASN][1000 genomes]
rs1128712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459688	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459930	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461148	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461195	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463268	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17458	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2071572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278281	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288420	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288518	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2288528	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288529	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301278	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745922	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3786867	0.96[ASN][1000 genomes]
rs3803903	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3826887	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3848618	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3859544	0.94[ASN][1000 genomes]
rs56666700	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56726774	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58017412	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58218194	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58824375	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59663064	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60176657	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60799292	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61570139	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61704307	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247152	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247378	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7255625	0.93[ASN][1000 genomes]
rs8101500	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs890871	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9710458	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55684400-55686800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:55684800-55686200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:55684800-55686400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:55684800-55687000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:55684800-55687000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
6	chr19:55685000-55686400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
7	chr19:55685000-55686800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
8	chr19:55685200-55686800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:55685200-55690400	Weak transcription	Gastric	stomach
10	chr19:55685400-55686200	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr19:55685400-55687000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
12	chr19:55685400-55687000	Bivalent Enhancer	Placenta	Placenta
13	chr19:55685600-55686200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:55685600-55686200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr19:55685600-55686200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:55685600-55686200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr19:55685600-55686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:55685600-55686800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr19:55685600-55686800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr19:55685600-55687800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:55685600-55690400	Weak transcription	Pancreas	Pancrea
22	chr19:55685600-55690400	Weak transcription	Right Atrium	heart
23	chr19:55685800-55686200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr19:55685800-55686200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
25	chr19:55685800-55686200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr19:55685800-55686200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr19:55685800-55686200	Enhancers	HepG2	liver
28	chr19:55685800-55686400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
29	chr19:55685800-55686400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
30	chr19:55685800-55686800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:55685800-55686800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
32	chr19:55685800-55686800	Bivalent Enhancer	Spleen	Spleen
33	chr19:55685800-55687000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:55685800-55690200	Weak transcription	Osteobl	bone
35	chr19:55685800-55690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:55686000-55686200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:55686000-55686200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:55686000-55686200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:55686000-55686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:55686000-55686400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
41	chr19:55686000-55686400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:55686000-55686600	Active TSS	K562	blood
43	chr19:55686000-55686800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:55686000-55687000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:55686000-55687000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:55686000-55689200	Weak transcription	Hela-S3	cervix
47	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:55686000-55690200	Weak transcription	A549	lung
49	chr19:55686000-55690200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links