Variant report

Variant	rs1304062
Chromosome Location	chr20:16392109-16392110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPD	chr20:16392041-16392395	K562	blood:	n/a	n/a
2	PML	chr20:16391965-16392326	K562	blood:	n/a	n/a
3	NRF1	chr20:16392081-16392377	K562	blood:	n/a	n/a
4	POLR2A	chr20:16392000-16392336	K562	blood:	n/a	n/a
5	EP300	chr20:16391980-16392396	K562	blood:	n/a	n/a
6	JUND	chr20:16391997-16392426	K562	blood:	n/a	n/a
7	GATA2	chr20:16391943-16392392	K562	blood:	n/a	n/a
8	ZNF384	chr20:16392009-16392482	K562	blood:	n/a	n/a
9	TEAD4	chr20:16391898-16392443	K562	blood:	n/a	n/a
10	TEAD4	chr20:16391876-16392404	K562	blood:	n/a	n/a
11	STAT5A	chr20:16391952-16392365	K562	blood:	n/a	n/a
12	ZMIZ1	chr20:16391983-16392365	K562	blood:	n/a	n/a
13	ATF3	chr20:16392071-16392280	K562	blood:	n/a	n/a
14	TAL1	chr20:16391828-16392464	K562	blood:	n/a	n/a
15	POLR2A	chr20:16392030-16392257	K562	blood:	n/a	n/a
16	GATA1	chr20:16391660-16392517	PBDE	blood:	n/a	n/a
17	CEBPD	chr20:16391974-16392425	K562	blood:	n/a	n/a
18	NR2F2	chr20:16391958-16392358	K562	blood:	n/a	n/a
19	GATA1	chr20:16391806-16392414	K562	blood:	n/a	n/a
20	TRIM28	chr20:16391950-16392419	K562	blood:	n/a	n/a
21	POLR2A	chr20:16392022-16392399	K562	blood:	n/a	n/a
22	PML	chr20:16391972-16392390	K562	blood:	n/a	n/a
23	NR2F2	chr20:16391858-16392466	K562	blood:	n/a	n/a
24	CCNT2	chr20:16392025-16392389	K562	blood:	n/a	n/a
25	STAT5A	chr20:16391979-16392360	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16388888..16390666-chr20:16391458..16394236,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000221448	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1884598	1.00[CHB][hapmap]
rs2144887	1.00[CHB][hapmap]
rs2208056	1.00[CHB][hapmap]
rs2876428	1.00[CHB][hapmap]
rs4814482	1.00[CHB][hapmap]
rs6034466	1.00[CHB][hapmap]
rs6043944	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080215	1.00[CHB][hapmap]
rs6080280	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1304062	HSPC072	cis	parietal	SCAN
rs1304062	SPTLC3	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16346600-16393600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr20:16372600-16404600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:16375400-16392600	Weak transcription	NH-A	brain
4	chr20:16375400-16396400	Weak transcription	Stomach Mucosa	stomach
5	chr20:16378000-16404400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:16378800-16393400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr20:16379000-16392800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr20:16379200-16395800	Weak transcription	NHDF-Ad	bronchial
9	chr20:16381400-16399200	Weak transcription	HMEC	breast
10	chr20:16384000-16432600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr20:16385200-16404200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr20:16385400-16404200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:16386200-16404400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr20:16386400-16398600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr20:16386400-16404200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr20:16387000-16393000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr20:16387000-16399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr20:16387000-16399000	Weak transcription	Liver	Liver
19	chr20:16387000-16399000	Weak transcription	Pancreas	Pancrea
20	chr20:16387000-16399400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr20:16387000-16403000	Weak transcription	Fetal Stomach	stomach
22	chr20:16387000-16404200	Weak transcription	Gastric	stomach
23	chr20:16387000-16406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr20:16387200-16399600	Weak transcription	NHEK	skin
25	chr20:16387400-16392200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:16387400-16404000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr20:16387400-16404400	Weak transcription	Esophagus	oesophagus
28	chr20:16387400-16411800	Weak transcription	Colonic Mucosa	Colon
29	chr20:16388800-16399000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr20:16389400-16396200	Weak transcription	HepG2	liver
31	chr20:16389600-16404200	Weak transcription	A549	lung
32	chr20:16391000-16401800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr20:16391200-16392200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr20:16391200-16392400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr20:16391200-16392400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr20:16391200-16392400	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr20:16391200-16392400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr20:16391200-16392400	ZNF genes & repeats	Fetal Heart	heart
39	chr20:16391200-16392400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr20:16391200-16393000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:16391200-16393000	ZNF genes & repeats	Adipose Nuclei	Adipose
42	chr20:16391200-16393000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
43	chr20:16391200-16393000	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr20:16391200-16393800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr20:16391200-16394000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr20:16391400-16392200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:16391400-16392200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
48	chr20:16391400-16392400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr20:16391400-16392400	ZNF genes & repeats	Brain Hippocampus Middle	brain
50	chr20:16391400-16392400	ZNF genes & repeats	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links