Variant report

Variant	rs2749775
Chromosome Location	chr4:3355538-3355539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3354072..3356995-chr4:3479067..3480969,2	MCF-7	breast:
2	chr4:3292442..3295168-chr4:3354775..3356513,2	MCF-7	breast:
3	chr4:3355212..3358066-chr4:3437874..3440532,4	MCF-7	breast:
4	chr4:3346774..3348608-chr4:3355000..3357039,2	MCF-7	breast:
5	chr4:3354561..3356756-chr4:3362854..3364509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12640186	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12640526	0.99[ASN][1000 genomes]
rs12640721	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12643903	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16844197	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16844201	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.99[ASN][1000 genomes]
rs2281470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs2343799	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2749776	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2749786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857859	1.00[ASW][hapmap];0.95[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];0.89[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2857860	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129329	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3129330	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3129331	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3129332	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129333	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129336	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58949283	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62274923	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274924	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73193354	0.83[ASN][1000 genomes]
rs73193357	0.83[ASN][1000 genomes]
rs73193371	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73193372	0.92[ASN][1000 genomes]
rs881818	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2749775	RGS12	cis	cerebellum	SCAN
rs2749775	DOK7	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
2	chr4:3344400-3356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:3344400-3362400	Weak transcription	HSMMtube	muscle
4	chr4:3344400-3367600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:3346200-3355800	Weak transcription	Gastric	stomach
6	chr4:3346600-3363800	Weak transcription	Fetal Brain Female	brain
7	chr4:3346600-3364600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:3347400-3360800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:3347400-3364800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:3348200-3367400	Weak transcription	Fetal Heart	heart
11	chr4:3348400-3358000	Weak transcription	Fetal Lung	lung
12	chr4:3348400-3360600	Weak transcription	HSMM	muscle
13	chr4:3348400-3367600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:3350400-3364000	Weak transcription	Spleen	Spleen
15	chr4:3350800-3364200	Weak transcription	Pancreas	Pancrea
16	chr4:3350800-3367600	Weak transcription	Ovary	ovary
17	chr4:3351000-3358800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:3352400-3363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:3354200-3358400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:3354200-3363800	Weak transcription	Brain Germinal Matrix	brain
21	chr4:3354400-3355600	Enhancers	HepG2	liver
22	chr4:3354400-3357000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:3354600-3356000	Enhancers	Liver	Liver
24	chr4:3354600-3356000	Strong transcription	Fetal Stomach	stomach
25	chr4:3354600-3364600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:3354800-3368200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:3355000-3356800	Enhancers	HUVEC	blood vessel
28	chr4:3355000-3358400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:3355000-3367800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:3355200-3355600	Weak transcription	Lung	lung
31	chr4:3355200-3356000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:3355200-3356200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:3355200-3356600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:3355200-3368400	Weak transcription	Fetal Intestine Small	intestine
35	chr4:3355400-3356000	Strong transcription	Primary T cells from cord blood	blood
36	chr4:3355400-3356200	Enhancers	HMEC	breast
37	chr4:3355400-3356400	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links