Variant report

Variant	rs3995908
Chromosome Location	chr3:112998530-112998531
allele	C/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	RAD21	chr3:112998493-112998921	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr3:112998512-112998806	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr3:112998516-112998880	K562	blood:	n/a	n/a
4	RAD21	chr3:112998473-112998924	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:112998524-112998905	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112986625..112989851-chr3:112997054..112999009,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511324	0.90[EUR][1000 genomes]
rs13326562	0.81[EUR][1000 genomes]
rs1499898	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs16860720	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes]
rs16860734	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28679287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438134	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap]
rs6780720	1.00[CEU][hapmap]
rs6808103	1.00[CEU][hapmap]
rs7625829	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7629636	1.00[CEU][hapmap]
rs7652801	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9288980	0.90[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs9811168	0.81[EUR][1000 genomes]
rs9819129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820139	0.91[AFR][1000 genomes]
rs9820627	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823770	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831049	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832953	0.82[YRI][hapmap];0.95[AFR][1000 genomes]
rs9836199	0.81[EUR][1000 genomes]
rs9837357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840485	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851183	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs9852068	1.00[CEU][hapmap]
rs9853439	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863114	0.81[EUR][1000 genomes]
rs9864630	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872998	0.83[AFR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3995908	DUSP1	trans	brain	seeQTL
rs3995908	MIR331	trans	lymphoblastoid	seeQTL
rs3995908	SIK1	trans	brain	seeQTL
rs3995908	BTG2	trans	brain	seeQTL
rs3995908	CCL3L1	trans	brain	seeQTL
rs3995908	TNFRSF11B	trans	brain	seeQTL
rs3995908	CCL3	trans	brain	seeQTL
rs3995908	PHLDB2	trans	brain	seeQTL
rs3995908	FAT4	trans	brain	seeQTL
rs3995908	KLF4	trans	brain	seeQTL
rs3995908	OMD	trans	brain	seeQTL
rs3995908	PRG4	trans	brain	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:112990600-113004000	Weak transcription	NHEK	skin
5	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
7	chr3:112995200-112999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:112995200-113001200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
14	chr3:112995400-113035800	Weak transcription	Lung	lung
15	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:112995800-112999400	Weak transcription	Fetal Kidney	kidney
18	chr3:112995800-112999600	Weak transcription	HSMMtube	muscle
19	chr3:112995800-113004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:112995800-113006600	Weak transcription	Fetal Brain Male	brain
21	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
23	chr3:112996000-113000000	Weak transcription	Pancreas	Pancrea
24	chr3:112996000-113005800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
26	chr3:112996200-112999400	Weak transcription	Fetal Thymus	thymus
27	chr3:112996200-113000400	Weak transcription	Stomach Mucosa	stomach
28	chr3:112996200-113000400	Strong transcription	NHDF-Ad	bronchial
29	chr3:112996200-113001200	Strong transcription	Fetal Lung	lung
30	chr3:112996200-113002000	Weak transcription	NH-A	brain
31	chr3:112996200-113003000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:112996200-113004400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:112996200-113005800	Weak transcription	Osteobl	bone
34	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:112996400-113003600	Weak transcription	Brain Angular Gyrus	brain
36	chr3:112996400-113004600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:112996600-112998800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
39	chr3:112996600-113004200	Strong transcription	Colon Smooth Muscle	Colon
40	chr3:112996800-112998600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:112996800-113002000	Strong transcription	Fetal Intestine Large	intestine
42	chr3:112996800-113003200	Strong transcription	Esophagus	oesophagus
43	chr3:112996800-113004200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:112997000-112999400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:112997000-112999600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:112997000-113000000	Strong transcription	Adipose Nuclei	Adipose
47	chr3:112997000-113001400	Strong transcription	Ovary	ovary
48	chr3:112997000-113003000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:112997000-113003200	Strong transcription	Fetal Brain Female	brain
50	chr3:112997000-113003400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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