Variant report

Variant	rs6829807
Chromosome Location	chr4:85732535-85732536
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	chr4:85725097..85727859-chr4:85731433..85733600,2	K562	blood:

Variant related genes	Relation type
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11097028	0.83[EUR][1000 genomes]
rs12500519	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12501525	0.88[ASN][1000 genomes]
rs12502294	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12502409	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12511112	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs13108722	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13118671	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484661	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1508670	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs16995920	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17009317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17009334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2218323	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs35190829	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3747680	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs4383611	0.81[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs4590017	0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs55871210	0.83[EUR][1000 genomes]
rs58074983	0.81[EUR][1000 genomes]
rs6531783	0.84[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs67624868	0.81[EUR][1000 genomes]
rs6815917	0.81[EUR][1000 genomes]
rs6816534	0.81[EUR][1000 genomes]
rs6820517	0.81[EUR][1000 genomes]
rs6825852	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6838727	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858666	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72664957	0.85[EUR][1000 genomes]
rs7685537	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7692223	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7695054	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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
rs6829807	NCRNA00247	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85696400-85757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:85697400-85772800	Weak transcription	Small Intestine	intestine
3	chr4:85701600-85783000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:85704200-85739800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:85705200-85735200	Weak transcription	A549	lung
6	chr4:85705400-85770000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:85708600-85777400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:85708800-85741200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:85709000-85769600	Weak transcription	Right Ventricle	heart
10	chr4:85709000-85781600	Weak transcription	Esophagus	oesophagus
11	chr4:85709200-85749000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:85709200-85770200	Weak transcription	Psoas Muscle	Psoas
13	chr4:85722200-85733600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:85722200-85787600	Weak transcription	Gastric	stomach
15	chr4:85722400-85751800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:85722400-85762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:85723000-85742000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:85723000-85751200	Weak transcription	Fetal Heart	heart
19	chr4:85723000-85754800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:85723000-85821000	Weak transcription	Pancreas	Pancrea
21	chr4:85723200-85749600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:85723200-85770400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:85723200-85777000	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:85723400-85738800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:85724000-85749400	Weak transcription	Fetal Intestine Small	intestine
26	chr4:85724000-85752000	Weak transcription	Fetal Stomach	stomach
27	chr4:85724000-85781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:85724000-85786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:85724200-85761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:85724200-85769600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:85724600-85753000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:85724800-85739200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:85725200-85739600	Weak transcription	Brain Germinal Matrix	brain
34	chr4:85725600-85735400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:85725600-85735400	Weak transcription	NH-A	brain
36	chr4:85725800-85735200	Weak transcription	NHEK	skin
37	chr4:85725800-85735400	Weak transcription	Aorta	Aorta
38	chr4:85725800-85738000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:85726200-85735200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:85727400-85732800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:85727400-85735400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:85727600-85734800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:85727800-85783200	Weak transcription	Colonic Mucosa	Colon
44	chr4:85728800-85733800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:85729400-85735000	Strong transcription	HSMM	muscle
46	chr4:85729400-85735600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:85729600-85732800	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:85729800-85735200	Weak transcription	HSMMtube	muscle
49	chr4:85729800-85738400	Weak transcription	Left Ventricle	heart
50	chr4:85729800-85755800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links