Variant report

Variant	rs12866564
Chromosome Location	chr13:111065775-111065776
allele	A/G
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	CHD1	chr13:111063393-111066220	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111064820..111066912-chr13:111364451..111367008,2	K562	blood:
2	chr13:111063956..111066256-chr13:111066546..111068934,2	K562	blood:

Variant related genes	Relation type
ENSG00000238629	TF binding region
ENSG00000134905	Chromatin interaction
ENSG00000238629	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12867664	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868152	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12868452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35166119	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486743	1.00[CHB][hapmap]
rs61963221	0.89[ASN][1000 genomes]
rs6492269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7318486	1.00[CHB][hapmap]
rs7328770	1.00[CHB][hapmap]
rs9521753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][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	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2751128	chr13:111040798-111132490	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111050200-111066000	Enhancers	NHDF-Ad	bronchial
2	chr13:111050200-111075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:111056200-111066000	Enhancers	Lung	lung
4	chr13:111057800-111070400	Enhancers	Right Atrium	heart
5	chr13:111058000-111066000	Enhancers	HUVEC	blood vessel
6	chr13:111059400-111067000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr13:111060200-111067000	Enhancers	Right Ventricle	heart
8	chr13:111060200-111082800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:111061000-111077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:111061200-111065800	Enhancers	Colon Smooth Muscle	Colon
11	chr13:111061400-111065800	Enhancers	Rectal Smooth Muscle	rectum
12	chr13:111061600-111065800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:111061600-111069200	Weak transcription	Fetal Brain Male	brain
14	chr13:111061800-111066000	Enhancers	HSMM	muscle
15	chr13:111061800-111066200	Enhancers	NHLF	lung
16	chr13:111061800-111066800	Enhancers	Placenta	Placenta
17	chr13:111062000-111065800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:111062000-111065800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr13:111062000-111069000	Enhancers	Left Ventricle	heart
20	chr13:111062400-111066000	Enhancers	Ovary	ovary
21	chr13:111062800-111068400	Weak transcription	Gastric	stomach
22	chr13:111063600-111065800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:111063800-111080800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:111064200-111078000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr13:111064400-111065800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:111064400-111066000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr13:111064400-111068200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr13:111064400-111069800	Weak transcription	Small Intestine	intestine
29	chr13:111064600-111066000	Enhancers	Adipose Nuclei	Adipose
30	chr13:111064600-111067400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:111064600-111068000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr13:111064800-111065800	Genic enhancers	NH-A	brain
33	chr13:111064800-111069800	Weak transcription	GM12878-XiMat	blood
34	chr13:111064800-111071800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:111065000-111065800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr13:111065000-111066000	Enhancers	HSMMtube	muscle
37	chr13:111065000-111066200	Enhancers	A549	lung
38	chr13:111065000-111070400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr13:111065000-111071000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:111065000-111071400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:111065000-111077000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr13:111065000-111077400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:111065200-111065800	Genic enhancers	Fetal Stomach	stomach
44	chr13:111065200-111065800	Weak transcription	Spleen	Spleen
45	chr13:111065200-111066200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr13:111065200-111067200	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr13:111065200-111067200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr13:111065200-111067800	Weak transcription	HMEC	breast
49	chr13:111065200-111068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:111065200-111068200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links