Variant report

Variant	rs2029461
Chromosome Location	chr6:34105790-34105791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:34105785-34105835	LNCaP	prostate:	n/a
2	chr6:34105785-34105835	HAEpiC	amniotic membrane:	n/a
3	chr6:34105785-34105835	GM12891	blood:	n/a
4	chr6:34105785-34105835	RPTEC	kidney:	n/a
5	chr6:34105785-34105835	GM06990	blood:	n/a
6	chr6:34105785-34105835	NT2-D1	testis:	n/a
7	chr6:34105785-34105835	K562	blood:	n/a
8	chr6:34105785-34105835	A549	lung:	n/a
9	chr6:34105785-34105835	MCF-7	breast:	n/a
10	chr6:34105785-34105835	PrEC	prostate:	n/a
11	chr6:34105785-34105835	AoSMC	blood vessel:	n/a
12	chr6:34105785-34105835	AG04449	skin:	fetal
13	chr6:34105785-34105835	BE2_C	brain:	n/a
14	chr6:34105785-34105835	GM12878	blood:	n/a
15	chr6:34105785-34105835	PANC-1	pancreas:	n/a
16	chr6:34105785-34105835	HMEC	breast:	n/a
17	chr6:34105785-34105835	AG04450	lung:	fetal
18	chr6:34105785-34105835	HepG2	liver:	n/a
19	chr6:34105785-34105835	AG10803	skin:	n/a
20	chr6:34105785-34105835	HRE	kidney:	n/a
21	chr6:34105785-34105835	HCM	heart:	n/a
22	chr6:34105785-34105835	HCPEpiC	choroid plexus:	n/a
23	chr6:34105785-34105835	Hepatocyte	liver:	n/a
24	chr6:34105785-34105835	HRCEpiC	kidney:	n/a
25	chr6:34105785-34105835	Caco-2	colon:	n/a
26	chr6:34105785-34105835	Hela-S3	cervix:	n/a
27	chr6:34105785-34105835	Jurkat	blood:	n/a
28	chr6:34105785-34105835	SK-N-MC	brain:	n/a
29	chr6:34105785-34105835	HEEpiC	esophagus:	n/a
30	chr6:34105785-34105835	NHBE	bronchial:	n/a
31	chr6:34105785-34105835	HEK293	kidney:	embryo
32	chr6:34105785-34105835	PFSK-1	brain:	n/a
33	chr6:34105785-34105835	SK-N-SH	brain:	n/a
34	chr6:34105785-34105835	HCF	heart:	n/a
35	chr6:34105785-34105835	CMK	blood:	n/a
36	chr6:34105785-34105835	BJ	skin:	n/a
37	chr6:34105785-34105835	NB4	blood:	n/a
38	chr6:34105785-34105835	T-47D	breast:	n/a
39	chr6:34105785-34105835	HUVEC	blood vessel:	n/a
40	chr6:34105785-34105835	ovcar-3	ovarian:	n/a
41	chr6:34105785-34105835	SK-N-SH_RA	brain:	n/a
42	chr6:34105785-34105835	GM19239	blood:	n/a
43	chr6:34105785-34105835	AG09319	gingival:	n/a
44	chr6:34105785-34105835	MCF10A-Er-Src	breast:	n/a
45	chr6:34105785-34105835	HIPEpiC	eye:	n/a
46	chr6:34105785-34105835	HPAEpiC	pulmonary alveolar:	n/a
47	chr6:34105785-34105835	ECC-1	luminal epithelium:	n/a
48	chr6:34105785-34105835	U87	brain:	n/a
49	chr6:34105785-34105835	HNPCEpiC	eye:	n/a
50	chr6:34105785-34105835	GM12892	blood:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34094147..34097219-chr6:34104417..34107232,3	K562	blood:
2	chr6:34094975..34100252-chr6:34102486..34107232,5	K562	blood:
3	chr6:34105117..34107025-chr6:34191466..34193901,2	K562	blood:
4	chr6:34100738..34104812-chr6:34105536..34108241,3	MCF-7	breast:
5	chr6:34063467..34066322-chr6:34104288..34107163,2	MCF-7	breast:

No data

Variant related genes	Relation type
GRM4	CpG island
ENSG00000124493	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1873246	0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2029457	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029459	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2029460	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2029462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2046821	0.84[ASN][1000 genomes]
rs2499720	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2499724	0.87[GIH][hapmap]
rs2499725	0.82[GIH][hapmap]
rs2499726	0.82[GIH][hapmap]
rs2499729	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2499730	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs2499731	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2499732	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs4713744	0.82[ASN][1000 genomes]
rs6918514	0.82[ASN][1000 genomes]
rs6918977	0.82[ASN][1000 genomes]
rs6928019	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs730638	0.90[JPT][hapmap]
rs744102	0.90[JPT][hapmap]
rs914813	0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9380409	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462900	chr6:33932442-34195011	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv602843	chr6:33932442-34195011	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv432881	chr6:34026522-34213822	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv885780	chr6:34050917-34131376	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv462902	chr6:34056726-34195011	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv602862	chr6:34056726-34195011	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2029461	BTBD9	cis	parietal	SCAN
rs2029461	FKBP5	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34099600-34106200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:34100200-34106000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:34101600-34110200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:34101800-34108800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr6:34102000-34107400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:34103800-34110400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:34104000-34107600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:34104400-34107800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:34104400-34111400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:34104600-34106000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:34104600-34106000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:34104600-34106400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:34104600-34107800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:34105000-34106000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:34105000-34107600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:34105400-34105800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:34105600-34105800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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