Variant report

Variant	rs28627331
Chromosome Location	chr4:119665345-119665346
allele	C/G/T
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	SPI1	chr4:119665015-119665368	HL-60	blood:	n/a	n/a
2	FOS	chr4:119665054-119665394	HUVEC	blood vessel:	n/a	chr4:119665275-119665286
3	POLR2A	chr4:119664521-119665636	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:119660361..119663221-chr4:119664884..119666730,2	MCF-7	breast:
2	chr4:119657933..119660578-chr4:119663582..119666420,2	K562	blood:
3	chr4:119657007..119658653-chr4:119665008..119667662,2	MCF-7	breast:

Variant related genes	Relation type
SEC24D	TF binding region
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10001115	0.88[EUR][1000 genomes]
rs10018977	0.88[EUR][1000 genomes]
rs10019311	0.88[EUR][1000 genomes]
rs10025640	0.88[EUR][1000 genomes]
rs11098451	0.95[EUR][1000 genomes]
rs11931194	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11938970	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17257039	1.00[AFR][1000 genomes]
rs17257945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17258050	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17258106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17258830	0.88[EUR][1000 genomes]
rs17259173	0.86[EUR][1000 genomes]
rs17259284	0.88[EUR][1000 genomes]
rs17323012	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17323034	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17323877	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17324807	0.88[EUR][1000 genomes]
rs17324821	0.88[EUR][1000 genomes]
rs17324884	0.88[EUR][1000 genomes]
rs17324968	0.88[EUR][1000 genomes]
rs17325017	0.88[EUR][1000 genomes]
rs17325129	0.88[EUR][1000 genomes]
rs17325192	0.88[EUR][1000 genomes]
rs28595532	0.95[EUR][1000 genomes]
rs28600971	0.95[EUR][1000 genomes]
rs28797314	0.88[EUR][1000 genomes]
rs28837152	0.88[EUR][1000 genomes]
rs41455648	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55633605	0.88[EUR][1000 genomes]
rs55634130	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55640619	0.88[EUR][1000 genomes]
rs55649377	0.88[EUR][1000 genomes]
rs55668908	0.88[EUR][1000 genomes]
rs55671478	0.88[EUR][1000 genomes]
rs55704595	0.88[EUR][1000 genomes]
rs55726697	0.88[EUR][1000 genomes]
rs55744948	0.88[EUR][1000 genomes]
rs55758547	0.88[EUR][1000 genomes]
rs55794497	0.88[EUR][1000 genomes]
rs55806110	0.88[EUR][1000 genomes]
rs55823625	0.88[EUR][1000 genomes]
rs55869953	0.88[EUR][1000 genomes]
rs55901549	0.88[EUR][1000 genomes]
rs55913633	0.88[EUR][1000 genomes]
rs55985953	0.88[EUR][1000 genomes]
rs56000725	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56027489	0.88[EUR][1000 genomes]
rs56042726	0.82[EUR][1000 genomes]
rs56046449	0.88[EUR][1000 genomes]
rs56046676	0.88[EUR][1000 genomes]
rs56104443	0.88[EUR][1000 genomes]
rs56117870	0.84[EUR][1000 genomes]
rs56124677	0.88[EUR][1000 genomes]
rs56150431	0.88[EUR][1000 genomes]
rs56162974	0.88[EUR][1000 genomes]
rs56212415	0.88[EUR][1000 genomes]
rs56225646	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56227053	0.88[EUR][1000 genomes]
rs56252481	0.88[EUR][1000 genomes]
rs56264833	0.84[EUR][1000 genomes]
rs56283736	0.88[EUR][1000 genomes]
rs56291421	0.88[EUR][1000 genomes]
rs56302493	0.88[EUR][1000 genomes]
rs56302600	0.88[EUR][1000 genomes]
rs56303276	0.88[EUR][1000 genomes]
rs56309519	0.88[EUR][1000 genomes]
rs56322132	0.88[EUR][1000 genomes]
rs56331118	0.88[EUR][1000 genomes]
rs56342843	0.88[EUR][1000 genomes]
rs56359736	0.88[EUR][1000 genomes]
rs56364904	0.88[EUR][1000 genomes]
rs56388366	0.88[EUR][1000 genomes]
rs56389935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56762141	0.88[EUR][1000 genomes]
rs6818519	0.88[EUR][1000 genomes]
rs73842212	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73842253	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
3	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
4	chr4:119630400-119674200	Weak transcription	A549	lung
5	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
6	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
9	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:119646200-119667000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:119649200-119666800	Weak transcription	Psoas Muscle	Psoas
15	chr4:119649200-119670600	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:119649200-119675200	Weak transcription	Brain Substantia Nigra	brain
17	chr4:119649200-119687600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:119649200-119693600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:119650600-119668400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:119651800-119665400	Strong transcription	HUVEC	blood vessel
21	chr4:119651800-119672600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr4:119651800-119687400	Weak transcription	Thymus	Thymus
23	chr4:119652000-119672400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:119653400-119668400	Strong transcription	HepG2	liver
25	chr4:119654400-119666200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:119654400-119672600	Strong transcription	NH-A	brain
27	chr4:119654400-119687400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:119654800-119676000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:119655400-119672800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr4:119655600-119665400	Strong transcription	Fetal Muscle Leg	muscle
31	chr4:119656200-119667800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:119659000-119667200	Strong transcription	HSMMtube	muscle
33	chr4:119659200-119668000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:119659600-119666600	Weak transcription	Right Ventricle	heart
35	chr4:119659600-119690400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:119660000-119672800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:119660200-119668000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:119660400-119673600	Strong transcription	Fetal Intestine Large	intestine
39	chr4:119660400-119688200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:119660400-119689800	Weak transcription	Brain Angular Gyrus	brain
41	chr4:119660600-119667600	Weak transcription	K562	blood
42	chr4:119660800-119667800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:119661000-119667800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:119661600-119671200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:119661800-119666400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:119661800-119671400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:119661800-119672800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:119661800-119684600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:119662000-119667800	Weak transcription	Fetal Thymus	thymus
50	chr4:119662000-119671200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links