Variant report

Variant	rs11946728
Chromosome Location	chr4:175138239-175138240
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:175132325..175134757-chr4:175137089..175139873,3	K562	blood:
2	chr4:175137442..175140324-chr4:175142017..175143698,2	K562	blood:
3	chr4:175112932..175114755-chr4:175136391..175138788,2	K562	blood:
4	chr4:175132325..175133854-chr4:175137410..175139370,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10034021	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10520275	0.88[CEU][hapmap]
rs10565	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11133035	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929798	1.00[CHB][hapmap]
rs11933187	1.00[CHB][hapmap]
rs11942947	1.00[CHB][hapmap]
rs11944262	0.81[MEX][hapmap]
rs13101580	1.00[CHB][hapmap];0.88[MEX][hapmap]
rs13128257	0.88[CEU][hapmap]
rs13150997	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17291087	0.88[CEU][hapmap]
rs17291128	0.88[CEU][hapmap]
rs17291408	0.88[CEU][hapmap]
rs17357120	0.82[MEX][hapmap]
rs1995749	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2332836	0.94[MEX][hapmap]
rs4287982	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4695915	0.88[CEU][hapmap]
rs4695918	0.83[MEX][hapmap]
rs4695919	1.00[CHB][hapmap]
rs4695922	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs6553777	0.88[CEU][hapmap]
rs6824643	0.88[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs6851312	0.88[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs7661236	0.88[CEU][hapmap]
rs7669484	0.88[CEU][hapmap]
rs7678305	0.83[MEX][hapmap]

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	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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
3	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11946728	CEP44	cis	Thyroid	GTEx
rs11946728	KIAA1712	cis	parietal	SCAN
rs11946728	KIAA1712	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175136000-175138400	Weak transcription	Aorta	Aorta
2	chr4:175137000-175138800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:175137200-175138400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr4:175137200-175138400	Bivalent Enhancer	Fetal Stomach	stomach
5	chr4:175137200-175139200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr4:175137400-175138400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr4:175137400-175138400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr4:175137400-175138400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
9	chr4:175137400-175138400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:175137400-175138400	Bivalent Enhancer	Liver	Liver
11	chr4:175137400-175138600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:175137400-175138600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr4:175137400-175139600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:175137400-175139600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr4:175137600-175138400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr4:175137600-175138400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
17	chr4:175137600-175138400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr4:175137600-175138400	Bivalent Enhancer	Ovary	ovary
19	chr4:175137600-175138600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr4:175137600-175138600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr4:175137600-175138600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr4:175137600-175139200	Bivalent Enhancer	Fetal Thymus	thymus
23	chr4:175137600-175139400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:175137600-175139800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr4:175137800-175138400	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr4:175137800-175138600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:175137800-175138600	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr4:175137800-175138800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr4:175137800-175139400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:175137800-175139600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr4:175137800-175139600	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr4:175137800-175139800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:175138000-175138400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:175138000-175138400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:175138000-175138400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
36	chr4:175138000-175138400	Bivalent Enhancer	Left Ventricle	heart
37	chr4:175138000-175138600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:175138000-175138600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
39	chr4:175138000-175138600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:175138000-175138600	Bivalent Enhancer	Brain Substantia Nigra	brain
41	chr4:175138000-175138600	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr4:175138000-175138600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
43	chr4:175138000-175138800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:175138000-175138800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:175138000-175139200	Bivalent Enhancer	Spleen	Spleen
46	chr4:175138000-175139400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
47	chr4:175138000-175139600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:175138000-175139600	Bivalent Enhancer	Esophagus	oesophagus
49	chr4:175138000-175139800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr4:175138000-175139800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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