Variant report

Variant	rs13390860
Chromosome Location	chr2:144940576-144940577
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	CEBPB	chr2:144940529-144940617	HepG2	liver:	n/a	chr2:144940547-144940560 chr2:144940548-144940559
2	CEBPB	chr2:144940548-144940601	K562	blood:	n/a	chr2:144940548-144940559

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:144939747..144942028-chr2:144942409..144944936,2	K562	blood:

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10188875	1.00[AMR][1000 genomes]
rs10196936	1.00[AMR][1000 genomes]
rs12327993	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs13390689	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs2058910	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1005376	chr2:144803630-144968946	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1013338	chr2:144806920-144969818	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv834396	chr2:144842187-145019465	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
13	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
14	esv3334733	chr2:144939582-144941530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13390860	HBD	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144923600-144941200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:144923800-144955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:144928000-144941400	Weak transcription	Lung	lung
4	chr2:144928000-144943400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:144928200-144965400	Weak transcription	Left Ventricle	heart
6	chr2:144929600-144941200	Weak transcription	Fetal Brain Female	brain
7	chr2:144931200-144941400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:144931200-144951800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:144931400-144973800	Weak transcription	Ovary	ovary
10	chr2:144931600-144941400	Weak transcription	Brain Angular Gyrus	brain
11	chr2:144931600-144944600	Weak transcription	Liver	Liver
12	chr2:144932000-144941200	Weak transcription	Adipose Nuclei	Adipose
13	chr2:144932000-144960600	Weak transcription	HSMMtube	muscle
14	chr2:144932000-144965000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:144932200-144955400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:144934800-144940800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:144936400-144940800	Weak transcription	Primary T cells from cord blood	blood
18	chr2:144936400-144941400	Weak transcription	Fetal Lung	lung
19	chr2:144936600-144941000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:144936800-144941000	Weak transcription	Primary B cells from cord blood	blood
21	chr2:144936800-144941200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:144937600-144955400	Weak transcription	Fetal Intestine Small	intestine
23	chr2:144938400-144940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:144938800-144940800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:144938800-144941000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:144938800-144941400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:144939200-144941200	Weak transcription	NHDF-Ad	bronchial
28	chr2:144939200-144951800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:144939400-144941400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:144940200-144955600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links