Variant report

Variant	rs60787284
Chromosome Location	chr4:129730104-129730105
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr4:129730034-129730194	MCF10A-Er-Src	breast:	n/a	n/a
2	SMC3	chr4:129729992-129732822	SK-N-SH	brain:	n/a	chr4:129732413-129732423

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:128980795..128984031-chr4:129730059..129735028,7	K562	blood:
2	chr4:129374782..129377512-chr4:129729521..129732215,3	K562	blood:
3	chr4:129472709..129474756-chr4:129728389..129731319,2	MCF-7	breast:
4	chr4:129518963..129527383-chr4:129727996..129735335,14	K562	blood:
5	chr4:129206178..129209105-chr4:129728853..129732712,4	K562	blood:
6	chr4:129376012..129378140-chr4:129729596..129731686,2	K562	blood:
7	chr4:129207558..129209105-chr4:129728853..129730896,2	K562	blood:
8	chr4:129472659..129478043-chr4:129729703..129733779,4	K562	blood:
9	chr4:129348880..129349601-chr4:129730054..129731203,4	MCF-7	breast:

No data

Variant related genes	Relation type
JADE1	TF binding region
ENSG00000251432	Chromatin interaction
ENSG00000248802	Chromatin interaction
ENSG00000273077	Chromatin interaction
ENSG00000164040	Chromatin interaction
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs17013725	1.00[EUR][1000 genomes]
rs17013730	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013733	1.00[EUR][1000 genomes]
rs17013736	1.00[EUR][1000 genomes]
rs17013744	1.00[EUR][1000 genomes]
rs17013759	1.00[EUR][1000 genomes]
rs17013765	1.00[EUR][1000 genomes]
rs17013766	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013768	1.00[ASN][1000 genomes]
rs17013775	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013777	1.00[EUR][1000 genomes]
rs17013779	1.00[EUR][1000 genomes]
rs17013786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013787	1.00[EUR][1000 genomes]
rs17013789	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013807	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013811	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013815	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013817	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013825	1.00[EUR][1000 genomes]
rs17013827	1.00[EUR][1000 genomes]
rs17013835	1.00[EUR][1000 genomes]
rs17013841	1.00[EUR][1000 genomes]
rs17013844	1.00[EUR][1000 genomes]
rs17013847	1.00[EUR][1000 genomes]
rs17013848	1.00[EUR][1000 genomes]
rs17013849	1.00[EUR][1000 genomes]
rs17013852	1.00[EUR][1000 genomes]
rs17013854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013857	1.00[EUR][1000 genomes]
rs17013862	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013866	1.00[EUR][1000 genomes]
rs17013872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013873	1.00[EUR][1000 genomes]
rs17013877	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013882	1.00[EUR][1000 genomes]
rs17013894	1.00[EUR][1000 genomes]
rs17013895	1.00[EUR][1000 genomes]
rs17013898	1.00[EUR][1000 genomes]
rs17013899	1.00[EUR][1000 genomes]
rs17013903	1.00[EUR][1000 genomes]
rs17303098	1.00[EUR][1000 genomes]
rs2004378	1.00[EUR][1000 genomes]
rs28635430	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816604	1.00[ASN][1000 genomes]
rs56180223	1.00[ASN][1000 genomes]
rs57153966	1.00[EUR][1000 genomes]
rs57547066	1.00[EUR][1000 genomes]
rs58296567	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58580868	1.00[EUR][1000 genomes]
rs58593491	1.00[EUR][1000 genomes]
rs58728331	1.00[EUR][1000 genomes]
rs58755790	1.00[EUR][1000 genomes]
rs58922070	1.00[EUR][1000 genomes]
rs58981205	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59682469	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61306978	1.00[EUR][1000 genomes]
rs61620977	1.00[EUR][1000 genomes]
rs61696721	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813405	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827804	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848234	1.00[EUR][1000 genomes]
rs6850940	1.00[EUR][1000 genomes]
rs6855813	1.00[EUR][1000 genomes]
rs73846991	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73850003	1.00[ASN][1000 genomes]
rs73850004	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682356	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129723600-129730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:129724800-129730600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:129725000-129730400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:129725200-129730400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:129725400-129730200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:129725400-129730200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:129725400-129730400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:129725400-129730400	Weak transcription	Stomach Mucosa	stomach
9	chr4:129725600-129730200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:129725600-129730200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:129725600-129730200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:129725600-129730400	Weak transcription	Fetal Intestine Small	intestine
13	chr4:129726200-129730200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:129726200-129730200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:129726200-129730400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:129726200-129730400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:129726200-129730800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:129726200-129731200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:129726400-129730200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:129726400-129730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:129726800-129730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:129727200-129730400	Enhancers	Fetal Heart	heart
23	chr4:129727400-129730400	Weak transcription	Placenta	Placenta
24	chr4:129727400-129730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:129728000-129730200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:129728400-129730200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:129729000-129730200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:129729800-129730400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:129730000-129730200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr4:129730000-129730200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:129730000-129730200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:129730000-129730200	Enhancers	Adipose Nuclei	Adipose
33	chr4:129730000-129730200	Enhancers	A549	lung
34	chr4:129730000-129730200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr4:129730000-129730200	Enhancers	NHLF	lung
36	chr4:129730000-129730400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr4:129730000-129730400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:129730000-129730400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr4:129730000-129730400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr4:129730000-129730400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:129730000-129730400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:129730000-129730400	Enhancers	Colon Smooth Muscle	Colon
43	chr4:129730000-129730400	Enhancers	Dnd41	blood
44	chr4:129730000-129730400	Enhancers	Hela-S3	cervix
45	chr4:129730000-129730600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:129730000-129734000	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links