Variant report

Variant	rs6858666
Chromosome Location	chr4:85729936-85729937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10007879	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10856851	0.82[AMR][1000 genomes]
rs10856852	0.83[JPT][hapmap];0.96[MEX][hapmap]
rs11097024	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11097026	0.84[AMR][1000 genomes]
rs12511112	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13114115	0.82[AMR][1000 genomes]
rs13118671	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13141322	0.82[AMR][1000 genomes]
rs13145705	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1385263	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1484660	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1484661	0.91[JPT][hapmap]
rs1508670	0.81[JPT][hapmap]
rs17009247	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17009249	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17009317	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs17009334	0.90[JPT][hapmap]
rs17009341	0.88[ASW][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap]
rs2046402	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2046404	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs2170935	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2218323	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs2869216	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3098928	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3747680	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs4131745	0.81[AMR][1000 genomes]
rs4529041	0.81[EUR][1000 genomes]
rs4533765	0.81[JPT][hapmap];0.96[MEX][hapmap]
rs6531775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531777	0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs6531782	0.83[JPT][hapmap];0.91[MEX][hapmap]
rs67045782	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6825852	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6829807	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6835046	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838727	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs6839516	0.83[EUR][1000 genomes]
rs6847067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847564	0.95[JPT][hapmap]
rs6853486	0.83[CEU][hapmap];0.91[MEX][hapmap]
rs6857555	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72664926	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72664934	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7654035	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs7661609	0.88[ASW][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.80[YRI][hapmap]
rs7663580	0.83[JPT][hapmap];0.95[MEX][hapmap]
rs7668460	0.82[EUR][1000 genomes]
rs7685537	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7694949	0.88[ASW][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.80[YRI][hapmap]
rs7699226	0.82[CHB][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]

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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv427684	chr4:85668487-85863446	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6858666	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85683800-85732000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:85696400-85757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:85697400-85772800	Weak transcription	Small Intestine	intestine
4	chr4:85701600-85783000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:85702200-85732200	Weak transcription	Spleen	Spleen
6	chr4:85704200-85739800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:85705200-85735200	Weak transcription	A549	lung
8	chr4:85705400-85770000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:85708600-85731000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:85708600-85777400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:85708800-85741200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:85709000-85731000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:85709000-85769600	Weak transcription	Right Ventricle	heart
14	chr4:85709000-85781600	Weak transcription	Esophagus	oesophagus
15	chr4:85709200-85749000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:85709200-85770200	Weak transcription	Psoas Muscle	Psoas
17	chr4:85722200-85733600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:85722200-85787600	Weak transcription	Gastric	stomach
19	chr4:85722400-85731000	Weak transcription	HepG2	liver
20	chr4:85722400-85751800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:85722400-85762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:85722600-85731000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:85722800-85730400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:85723000-85731000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:85723000-85742000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:85723000-85751200	Weak transcription	Fetal Heart	heart
27	chr4:85723000-85754800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:85723000-85821000	Weak transcription	Pancreas	Pancrea
29	chr4:85723200-85749600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:85723200-85770400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:85723200-85777000	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:85723400-85738800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:85723800-85730200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:85723800-85731000	Weak transcription	Lung	lung
35	chr4:85724000-85749400	Weak transcription	Fetal Intestine Small	intestine
36	chr4:85724000-85752000	Weak transcription	Fetal Stomach	stomach
37	chr4:85724000-85781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:85724000-85786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:85724200-85761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:85724200-85769600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr4:85724600-85730000	Weak transcription	Adipose Nuclei	Adipose
42	chr4:85724600-85730400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:85724600-85753000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:85724800-85739200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:85725200-85739600	Weak transcription	Brain Germinal Matrix	brain
46	chr4:85725400-85730200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:85725600-85730200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:85725600-85735400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:85725600-85735400	Weak transcription	NH-A	brain
50	chr4:85725800-85730200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links