Variant report

Variant	rs4127813
Chromosome Location	chr14:56604125-56604126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56597393..56599365-chr14:56602451..56604524,3	K562	blood:
2	chr14:56602302..56604892-chr14:56607961..56609487,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10144612	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10483656	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1427556	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap]
rs17688725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17688801	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17689278	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17761563	1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.81[YRI][hapmap]
rs17762499	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17762733	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17832675	0.81[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1951955	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2035283	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2343376	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28712711	0.81[EUR][1000 genomes]
rs2880615	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3850298	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3912203	1.00[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8020301	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4127813	PSMC6	cis	cerebellum	SCAN
rs4127813	ERO1L	cis	parietal	SCAN
rs4127813	C14orf166	cis	cerebellum	SCAN
rs4127813	C14orf37	cis	cerebellum	SCAN
rs4127813	ARID4A	cis	cerebellum	SCAN
rs4127813	MAPK1IP1L	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56593200-56612800	Weak transcription	Brain Angular Gyrus	brain
2	chr14:56595600-56607000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr14:56596600-56615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:56596800-56604200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:56597000-56611800	Weak transcription	Lung	lung
6	chr14:56597200-56605600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr14:56597200-56607200	Enhancers	Dnd41	blood
8	chr14:56598200-56606600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr14:56598400-56604200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr14:56599000-56604600	Weak transcription	Brain Anterior Caudate	brain
11	chr14:56599200-56606600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr14:56599400-56604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:56599400-56604200	Weak transcription	Brain Hippocampus Middle	brain
14	chr14:56599400-56614800	Weak transcription	Brain Substantia Nigra	brain
15	chr14:56599400-56615000	Weak transcription	Left Ventricle	heart
16	chr14:56599600-56605600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:56600000-56607800	Enhancers	Primary hematopoietic stem cells	blood
18	chr14:56600400-56604200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr14:56600400-56605400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:56600400-56606800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:56600600-56604200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr14:56600600-56604600	Weak transcription	Thymus	Thymus
23	chr14:56600600-56605800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:56600600-56605800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:56600600-56608400	Weak transcription	Gastric	stomach
26	chr14:56600600-56615000	Weak transcription	Right Atrium	heart
27	chr14:56601000-56607800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr14:56601200-56606000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr14:56601800-56605000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr14:56602000-56604600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:56602200-56604400	Enhancers	Colon Smooth Muscle	Colon
32	chr14:56602400-56604400	Enhancers	Fetal Kidney	kidney
33	chr14:56603000-56604800	Enhancers	Fetal Stomach	stomach
34	chr14:56603000-56607000	Enhancers	Fetal Brain Male	brain
35	chr14:56603400-56604400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr14:56603400-56604600	Enhancers	Brain Germinal Matrix	brain
37	chr14:56603400-56605000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr14:56603400-56605000	Enhancers	Primary B cells from cord blood	blood
39	chr14:56603400-56606000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr14:56603400-56606000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:56603400-56606000	Enhancers	Ovary	ovary
42	chr14:56603400-56607600	Enhancers	Fetal Brain Female	brain
43	chr14:56603600-56604200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr14:56603600-56604800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr14:56603600-56604800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr14:56603600-56604800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr14:56603600-56606000	Enhancers	Pancreas	Pancrea
48	chr14:56603600-56606400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr14:56603600-56607400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr14:56603800-56604200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links