Variant report

Variant	rs413120
Chromosome Location	chr6:13280641-13280642
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	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFOD1-1	chr6:13279527-13281388	ENSG00000215022.3

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1550526	0.83[CEU][hapmap]
rs202030	0.83[CEU][hapmap]
rs202038	0.83[CEU][hapmap]
rs202040	0.83[CEU][hapmap]
rs202042	1.00[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs202044	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs202045	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs202046	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs202051	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs202053	1.00[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs202070	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs202071	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs202072	1.00[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs202073	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs202077	0.82[EUR][1000 genomes]
rs375661	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs377704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs384730	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs405078	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs412787	0.84[LWK][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs417048	0.80[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs441213	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs442614	0.89[LWK][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs445591	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs445714	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs454563	0.83[CEU][hapmap]
rs4602719	0.83[CEU][hapmap]
rs495895	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8541	0.83[CEU][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs413120	EDN1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
3	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
6	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:13270200-13291600	Weak transcription	HSMM	muscle
9	chr6:13270400-13282000	Weak transcription	Ovary	ovary
10	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
11	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
14	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:13273400-13286800	Weak transcription	Liver	Liver
16	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
17	chr6:13274000-13282600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:13274000-13283800	Weak transcription	Brain Substantia Nigra	brain
19	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
22	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
25	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
27	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:13275000-13282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:13275000-13285000	Weak transcription	Fetal Intestine Small	intestine
30	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:13275000-13287000	Weak transcription	Gastric	stomach
32	chr6:13275200-13286400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:13275600-13281000	Weak transcription	Placenta	Placenta
34	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:13275800-13282200	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:13276000-13282800	Weak transcription	Right Ventricle	heart
39	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr6:13276200-13281400	Genic enhancers	Primary B cells from cord blood	blood
41	chr6:13276600-13281000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:13277200-13281600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:13277200-13282000	Strong transcription	Left Ventricle	heart
44	chr6:13277400-13281600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:13277400-13286200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr6:13277400-13287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:13277600-13281800	Strong transcription	Aorta	Aorta
48	chr6:13277600-13282400	Weak transcription	HepG2	liver
49	chr6:13277600-13284200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:13277800-13281000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links