Variant report

Variant	rs28549046
Chromosome Location	chr3:42647345-42647346
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	EGR1	chr3:42647332-42647660	K562	blood:	n/a	n/a
2	JUND	chr3:42646927-42647775	K562	blood:	n/a	chr3:42647535-42647547 chr3:42647537-42647545 chr3:42647538-42647545 chr3:42647535-42647546 chr3:42647536-42647546 chr3:42647537-42647545 chr3:42647536-42647546
3	RCOR1	chr3:42647057-42647679	K562	blood:	n/a	n/a
4	TEAD4	chr3:42647135-42647722	K562	blood:	n/a	n/a
5	CBX3	chr3:42647255-42647729	K562	blood:	n/a	n/a
6	EGR1	chr3:42647328-42647681	K562	blood:	n/a	n/a
7	TEAD4	chr3:42647045-42647742	K562	blood:	n/a	n/a
8	FOSL1	chr3:42647265-42647785	K562	blood:	n/a	chr3:42647535-42647547 chr3:42647537-42647545 chr3:42647538-42647545 chr3:42647536-42647546 chr3:42647537-42647545 chr3:42647536-42647546 chr3:42647535-42647546
9	TBL1XR1	chr3:42646645-42648020	K562	blood:	n/a	n/a
10	CCNT2	chr3:42647340-42647693	K562	blood:	n/a	n/a
11	GATA2	chr3:42647257-42647745	K562	blood:	n/a	chr3:42647538-42647547
12	JUN	chr3:42646847-42648314	K562	blood:	n/a	chr3:42647535-42647547 chr3:42647537-42647545 chr3:42647538-42647545 chr3:42647536-42647546 chr3:42647537-42647545 chr3:42647536-42647546
13	ATF3	chr3:42647324-42647752	K562	blood:	n/a	n/a
14	JUN	chr3:42647323-42647691	K562	blood:	n/a	chr3:42647535-42647547 chr3:42647537-42647545 chr3:42647538-42647545 chr3:42647536-42647546 chr3:42647537-42647545 chr3:42647536-42647546
15	TRIM28	chr3:42647001-42647786	K562	blood:	n/a	n/a
16	FOS	chr3:42647337-42647729	K562	blood:	n/a	chr3:42647535-42647547 chr3:42647537-42647545 chr3:42647538-42647545 chr3:42647536-42647546 chr3:42647537-42647545 chr3:42647536-42647546 chr3:42647535-42647546
17	RCOR1	chr3:42647136-42647735	K562	blood:	n/a	n/a
18	TAL1	chr3:42647306-42647690	K562	blood:	n/a	n/a
19	MAZ	chr3:42647313-42647691	K562	blood:	n/a	n/a
20	MYC	chr3:42647138-42647737	K562	blood:	n/a	n/a
21	EP300	chr3:42646939-42647973	K562	blood:	n/a	chr3:42647536-42647545
22	ZMIZ1	chr3:42647168-42647987	K562	blood:	n/a	n/a
23	ARID3A	chr3:42647088-42647906	K562	blood:	n/a	chr3:42647441-42647457
24	JUN	chr3:42647311-42647728	K562	blood:	n/a	chr3:42647535-42647547 chr3:42647537-42647545 chr3:42647538-42647545 chr3:42647536-42647546 chr3:42647537-42647545 chr3:42647536-42647546
25	ATF1	chr3:42647190-42647721	K562	blood:	n/a	n/a
26	POLR2A	chr3:42647304-42647701	K562	blood:	n/a	n/a
27	MAFF	chr3:42647254-42648012	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42632973..42636724-chr3:42645956..42649361,3	MCF-7	breast:

Variant related genes	Relation type
SEC22C	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10154957	1.00[AMR][1000 genomes]
rs13320598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13325536	1.00[AMR][1000 genomes]
rs28508060	1.00[AMR][1000 genomes]
rs580447	1.00[AMR][1000 genomes]
rs58273990	1.00[AMR][1000 genomes]
rs9812538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9812673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822273	1.00[AMR][1000 genomes]
rs9832720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9853946	1.00[AMR][1000 genomes]
rs9855071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869491	1.00[AMR][1000 genomes]
rs9876937	1.00[AMR][1000 genomes]
rs9884030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9985232	0.91[AFR][1000 genomes];1.00[AMR][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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' 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	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643000-42650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:42643000-42650000	Weak transcription	Esophagus	oesophagus
3	chr3:42643200-42648400	Weak transcription	Placenta	Placenta
4	chr3:42643200-42649600	Weak transcription	Lung	lung
5	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:42643400-42647800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:42643600-42648400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
9	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:42644000-42647600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:42644000-42648200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:42644000-42648400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:42644000-42649800	Weak transcription	Right Atrium	heart
14	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
18	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:42644200-42648000	Weak transcription	Fetal Intestine Large	intestine
20	chr3:42644200-42648400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:42644200-42648400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:42644200-42648400	Weak transcription	Thymus	Thymus
23	chr3:42644200-42649800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:42644200-42649800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:42644200-42655200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
28	chr3:42644400-42647400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:42644400-42653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:42644800-42648200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:42644800-42649600	Weak transcription	Left Ventricle	heart
32	chr3:42644800-42649600	Weak transcription	Ovary	ovary
33	chr3:42644800-42649800	Weak transcription	Small Intestine	intestine
34	chr3:42644800-42650200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
36	chr3:42644800-42660200	Weak transcription	NH-A	brain
37	chr3:42645000-42649400	Strong transcription	Primary B cells from cord blood	blood
38	chr3:42645200-42648400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:42645200-42652200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:42645200-42660200	Weak transcription	HMEC	breast
41	chr3:42645600-42647400	Genic enhancers	Hela-S3	cervix
42	chr3:42645600-42647600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:42645600-42648600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:42645600-42649400	Weak transcription	Fetal Stomach	stomach
45	chr3:42645600-42650400	Strong transcription	Fetal Thymus	thymus
46	chr3:42645600-42653400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr3:42645800-42647400	Genic enhancers	Dnd41	blood
48	chr3:42645800-42649800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:42646000-42647400	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:42646000-42647400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links