Variant report

Variant	rs2430979
Chromosome Location	chr11:65813383-65813384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr11:65811971-65813510	IMR90	lung:	n/a	chr11:65813062-65813071
2	CTCF	chr11:65813260-65813410	GM12872	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
2	chr11:65657526..65660220-chr11:65812973..65815737,3	MCF-7	breast:
3	chr11:65792176..65796965-chr11:65812595..65817477,5	MCF-7	breast:
4	chr11:65767772..65771693-chr11:65812597..65815090,3	MCF-7	breast:
5	chr11:65812922..65815510-chr11:65837744..65839701,2	K562	blood:
6	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:
7	chr11:65787106..65790003-chr11:65812691..65814392,2	MCF-7	breast:

No data

Variant related genes	Relation type
GAL3ST3	TF binding region
SF3B2	TF binding region
ENSG00000175115	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000175602	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1055615	1.00[CEU][hapmap]
rs10791838	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs10791840	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs10791841	0.97[EUR][1000 genomes]
rs10791845	0.89[GIH][hapmap]
rs10896075	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10896077	1.00[CEU][hapmap]
rs10896081	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs10896089	1.00[CEU][hapmap]
rs10896091	1.00[CEU][hapmap]
rs11227410	1.00[CEU][hapmap]
rs11227411	1.00[CEU][hapmap]
rs11227413	1.00[CEU][hapmap]
rs11227415	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs1125078	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11607393	0.92[CEU][hapmap]
rs12576969	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12790034	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12797282	0.87[EUR][1000 genomes]
rs1783569	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1815814	0.81[EUR][1000 genomes]
rs2155201	0.81[CEU][hapmap]
rs2236651	0.81[CEU][hapmap]
rs2236652	0.81[CEU][hapmap]
rs2270448	0.93[GIH][hapmap]
rs2293121	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs2452681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2452682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34274349	0.96[EUR][1000 genomes]
rs34450124	0.82[ASN][1000 genomes]
rs3814744	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3825067	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs3862386	0.93[CEU][hapmap]
rs4261293	0.97[EUR][1000 genomes]
rs4267077	0.93[EUR][1000 genomes]
rs4565902	0.97[EUR][1000 genomes]
rs4614460	0.91[EUR][1000 genomes]
rs476551	0.81[CEU][hapmap]
rs535395	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs61895582	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61895584	0.85[EUR][1000 genomes]
rs6591199	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6591201	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6591202	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6591203	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6591207	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs6591208	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs7110838	0.90[EUR][1000 genomes]
rs7120326	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs7120611	0.97[EUR][1000 genomes]
rs730787	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7925123	0.81[CEU][hapmap]
rs7931167	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7941469	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs7946917	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs7951770	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9326365	0.90[EUR][1000 genomes]
rs9645684	1.00[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	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2430979	ROM1	cis	parietal	SCAN
rs2430979	GSTM1	trans	lymphoblastoid	seeQTL
rs2430979	POLR2G	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65790400-65818600	Weak transcription	HSMM	muscle
2	chr11:65805000-65815800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65809800-65815800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:65811600-65814400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:65811800-65814200	Weak transcription	Brain Germinal Matrix	brain
6	chr11:65811800-65814600	Weak transcription	Fetal Brain Female	brain
7	chr11:65812000-65813400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr11:65812200-65814800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:65812400-65813400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:65812400-65813400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr11:65812400-65813400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr11:65812400-65813400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:65812400-65813400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr11:65812400-65813400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:65812400-65813400	Flanking Active TSS	Dnd41	blood
16	chr11:65812400-65813600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr11:65812400-65813600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:65812400-65813600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:65812400-65813600	Enhancers	Brain Cingulate Gyrus	brain
20	chr11:65812400-65814600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:65812400-65815200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:65812600-65814400	Enhancers	Fetal Intestine Small	intestine
23	chr11:65812800-65813400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:65812800-65813400	Enhancers	A549	lung
25	chr11:65812800-65813400	Enhancers	K562	blood
26	chr11:65812800-65813800	Bivalent Enhancer	HepG2	liver
27	chr11:65812800-65814400	Enhancers	Fetal Intestine Large	intestine
28	chr11:65812800-65815000	Weak transcription	Fetal Brain Male	brain
29	chr11:65812800-65815000	Weak transcription	Fetal Heart	heart
30	chr11:65812800-65816200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:65813000-65813400	Enhancers	Right Ventricle	heart
32	chr11:65813000-65813600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:65813000-65814000	Weak transcription	Right Atrium	heart
34	chr11:65813000-65814600	Weak transcription	GM12878-XiMat	blood
35	chr11:65813000-65814800	Weak transcription	Left Ventricle	heart
36	chr11:65813000-65815200	Weak transcription	Brain Angular Gyrus	brain
37	chr11:65813000-65815200	Weak transcription	Brain Anterior Caudate	brain
38	chr11:65813000-65815600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:65813000-65816200	Weak transcription	Brain Substantia Nigra	brain
40	chr11:65813000-65816600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:65813000-65818200	Weak transcription	Lung	lung
42	chr11:65813200-65813400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:65813200-65813400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr11:65813200-65813400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
45	chr11:65813200-65813600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:65813200-65814200	Weak transcription	Pancreas	Pancrea
47	chr11:65813200-65814400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:65813200-65814400	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:65813200-65815000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:65813200-65815200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links