Variant report

Variant	rs56243018
Chromosome Location	chr3:141101839-141101840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:141101806-141101986	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:141101694-141101924	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:141101398-141102196	U87	brain:	n/a	n/a
4	POLR2A	chr3:141101616-141105956	IMR90	lung:	n/a	n/a
5	POLR2A	chr3:141101478-141106905	GM19099	blood:	n/a	n/a
6	POLR2A	chr3:141101516-141106882	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:141101404-141102190	U87	brain:	n/a	n/a
8	NRF1	chr3:141101612-141102002	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:141101505-141108266	GM18505	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141100414..141103542-chr3:141104803..141108062,6	MCF-7	breast:
2	chr3:141100225..141102458-chr3:141109602..141112183,2	K562	blood:
3	chr3:141085900..141088726-chr3:141100588..141103501,2	MCF-7	breast:
4	chr3:141088231..141090050-chr3:141099495..141101974,2	K562	blood:
5	chr3:141099231..141102671-chr3:141118653..141123217,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1344673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16851397	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55715288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55750762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763780	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73872717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73872719	1.00[EUR][1000 genomes]

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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
2	chr3:141088000-141102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:141088000-141105200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:141088200-141102400	Weak transcription	Fetal Kidney	kidney
5	chr3:141088400-141102400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:141088400-141107600	Weak transcription	Small Intestine	intestine
7	chr3:141089200-141104800	Strong transcription	Fetal Intestine Large	intestine
8	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
9	chr3:141089400-141102200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:141089400-141104200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:141089600-141102400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:141089600-141102400	Weak transcription	Fetal Brain Male	brain
13	chr3:141089600-141102400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:141089600-141105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:141089800-141102600	Strong transcription	Fetal Intestine Small	intestine
16	chr3:141091000-141107200	Weak transcription	Liver	Liver
17	chr3:141092000-141105600	Weak transcription	Gastric	stomach
18	chr3:141092200-141102400	Strong transcription	HSMM	muscle
19	chr3:141092800-141102400	Weak transcription	Hela-S3	cervix
20	chr3:141093800-141102200	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr3:141094200-141102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:141094600-141104200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:141094800-141105600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:141094800-141112200	Weak transcription	Spleen	Spleen
25	chr3:141095200-141105600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:141095200-141105800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:141095400-141102400	Weak transcription	Fetal Stomach	stomach
28	chr3:141095400-141102600	Strong transcription	Placenta	Placenta
29	chr3:141096000-141104400	Weak transcription	Fetal Heart	heart
30	chr3:141096000-141111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:141096200-141102400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:141096200-141102400	Weak transcription	Colonic Mucosa	Colon
33	chr3:141096200-141106400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:141096800-141102600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:141097200-141105600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:141097800-141102400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr3:141098400-141105800	Weak transcription	Right Ventricle	heart
38	chr3:141098400-141107600	Weak transcription	Aorta	Aorta
39	chr3:141098600-141105200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:141098600-141105600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:141098600-141115200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:141099000-141110400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:141099200-141102800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:141099200-141104400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:141099400-141102200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:141099400-141104400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:141099400-141105800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:141099400-141106600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:141099600-141102400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:141099600-141104800	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links