Variant report

Variant	rs4901592
Chromosome Location	chr14:56055446-56055447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56055222..56057349-chr14:56060452..56063335,3	K562	blood:
2	chr14:56053879..56055533-chr14:56070490..56072513,2	K562	blood:
3	chr14:56047540..56051954-chr14:56053859..56059782,6	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10136386	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10136408	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs10146870	0.87[CEU][hapmap]
rs10444721	0.87[CEU][hapmap]
rs12587735	0.87[CEU][hapmap]
rs12882850	0.87[CEU][hapmap]
rs12891489	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs12893162	0.83[CEU][hapmap]
rs12897227	0.87[CEU][hapmap]
rs17684959	0.83[CEU][hapmap]
rs1951887	0.87[CEU][hapmap]
rs2296182	0.87[CEU][hapmap]
rs34872770	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3736877	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs3765515	0.87[CEU][hapmap]
rs3783654	0.82[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs4386042	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4457912	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4901593	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573042	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6573053	0.83[CEU][hapmap]
rs6573054	0.87[CEU][hapmap]
rs7158176	0.88[CEU][hapmap]
rs8007832	0.87[CEU][hapmap]
rs8011252	0.83[EUR][1000 genomes]
rs8011732	0.83[CEU][hapmap]
rs942317	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4901592	CNIH	cis	cerebellum	SCAN
rs4901592	GCH1	cis	cerebellum	SCAN
rs4901592	KTN1	cis	cerebellum	SCAN
rs4901592	FBXO34	cis	parietal	SCAN
rs4901592	KTN1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56048200-56068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:56048400-56056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr14:56048400-56068400	Weak transcription	Esophagus	oesophagus
4	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:56048600-56058400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:56048600-56060400	Weak transcription	Brain Substantia Nigra	brain
7	chr14:56048600-56070800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:56050000-56056000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr14:56050000-56056400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:56050400-56056200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr14:56050400-56056400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:56051000-56056800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr14:56051200-56057200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr14:56051200-56057600	Weak transcription	Spleen	Spleen
15	chr14:56051200-56058000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:56051200-56060200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr14:56051200-56066200	Weak transcription	Colonic Mucosa	Colon
18	chr14:56051200-56069000	Weak transcription	Primary B cells from cord blood	blood
19	chr14:56051400-56056000	Enhancers	Fetal Heart	heart
20	chr14:56051400-56060200	Weak transcription	K562	blood
21	chr14:56051600-56056400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:56051600-56059400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:56051600-56061600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:56051800-56056200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr14:56052000-56056200	Enhancers	NHEK	skin
26	chr14:56052000-56056400	Enhancers	NHLF	lung
27	chr14:56052000-56066200	Weak transcription	Pancreas	Pancrea
28	chr14:56052000-56068400	Weak transcription	Left Ventricle	heart
29	chr14:56052000-56080200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr14:56052200-56056200	Enhancers	HepG2	liver
31	chr14:56052200-56056400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:56052400-56056200	Enhancers	Adipose Nuclei	Adipose
33	chr14:56052400-56056200	Enhancers	Brain Anterior Caudate	brain
34	chr14:56052600-56055800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr14:56052600-56056000	Enhancers	Duodenum Mucosa	Duodenum
36	chr14:56052600-56056200	Enhancers	Rectal Smooth Muscle	rectum
37	chr14:56052800-56056200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr14:56053000-56057800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr14:56053000-56057800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr14:56053000-56057800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:56053000-56059000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:56053200-56055800	Enhancers	HSMMtube	muscle
43	chr14:56053200-56056400	Enhancers	HSMM	muscle
44	chr14:56053200-56057000	Weak transcription	HUVEC	blood vessel
45	chr14:56053200-56057800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:56053200-56058000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr14:56053200-56059800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr14:56053200-56069400	Weak transcription	Aorta	Aorta
49	chr14:56053800-56056000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr14:56054000-56056000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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