Variant report

Variant	rs1862942
Chromosome Location	chr3:120365010-120365011
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	GATA3	chr3:120364891-120365283	T-47D	breast:	n/a	n/a
2	GATA3	chr3:120364845-120365237	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
HGD	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17140347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1862938	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1862940	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2015444	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2081311	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2113470	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2194423	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2551575	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2551598	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2551607	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2551622	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733795	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35002954	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35447032	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4676817	1.00[JPT][hapmap]
rs4676818	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1862942	PARP9	cis	cerebellum	SCAN
rs1862942	CSTA	cis	cerebellum	SCAN
rs1862942	DTX3L	cis	cerebellum	SCAN
rs1862942	GTF2E1	cis	parietal	SCAN
rs1862942	NR1I2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120346400-120402200	Weak transcription	Gastric	stomach
2	chr3:120347400-120398000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:120355000-120368400	Strong transcription	HepG2	liver
4	chr3:120355600-120365200	Weak transcription	Fetal Stomach	stomach
5	chr3:120355600-120371200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:120355800-120368400	Weak transcription	Fetal Intestine Large	intestine
7	chr3:120355800-120369800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:120356200-120367000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:120356600-120378200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:120356800-120368200	Weak transcription	Fetal Intestine Small	intestine
11	chr3:120358400-120366200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:120358600-120369600	Strong transcription	Liver	Liver
13	chr3:120359200-120377600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:120360800-120372200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:120361000-120369600	Weak transcription	Pancreas	Pancrea
16	chr3:120361000-120372000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:120361800-120365200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:120361800-120365600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:120362000-120367400	Enhancers	K562	blood
20	chr3:120362000-120368600	Weak transcription	A549	lung
21	chr3:120363600-120365600	Enhancers	HSMMtube	muscle
22	chr3:120363600-120366200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:120363800-120371800	Weak transcription	Stomach Mucosa	stomach
24	chr3:120364000-120366000	Enhancers	Left Ventricle	heart
25	chr3:120364200-120366400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:120364200-120367000	Enhancers	Fetal Heart	heart
27	chr3:120364400-120365400	Weak transcription	Osteobl	bone
28	chr3:120364400-120365600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:120364400-120365600	Weak transcription	Adipose Nuclei	Adipose
30	chr3:120364400-120365600	Weak transcription	Right Atrium	heart
31	chr3:120364400-120367200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:120364600-120368400	Weak transcription	Ovary	ovary
33	chr3:120365000-120366200	Enhancers	Brain Angular Gyrus	brain

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