Variant report

Variant	rs13414307
Chromosome Location	chr2:40649084-40649085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10205556	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11901878	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs12052649	0.85[CHB][hapmap];0.81[YRI][hapmap]
rs12052650	0.85[CHB][hapmap];0.81[YRI][hapmap]
rs12052800	0.80[CHB][hapmap]
rs12105764	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12988659	0.85[CHB][hapmap]
rs13017237	0.80[CHB][hapmap];0.81[YRI][hapmap]
rs13418726	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs17025965	0.84[CHB][hapmap]
rs2888677	0.87[JPT][hapmap]
rs2888678	0.87[JPT][hapmap]
rs4366950	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4952621	0.85[CHB][hapmap]
rs6712702	0.89[CHD][hapmap]
rs6737011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7579930	0.94[CHB][hapmap]
rs7603114	0.85[CEU][hapmap]
rs9789739	0.80[CHB][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1007027	chr2:40627475-40649916	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13414307	SULT6B1	cis	parietal	SCAN
rs13414307	ABCG5	cis	cerebellum	SCAN
rs13414307	CCDC75	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40635800-40652600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr2:40642800-40654600	Weak transcription	HSMM	muscle
4	chr2:40644200-40656000	Weak transcription	HMEC	breast
5	chr2:40644200-40656400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:40644200-40658600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:40645000-40649600	Enhancers	Fetal Stomach	stomach
8	chr2:40645400-40649800	Enhancers	Colon Smooth Muscle	Colon
9	chr2:40645600-40650000	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:40646200-40655800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:40646400-40654200	Weak transcription	Fetal Brain Male	brain
12	chr2:40646400-40658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
14	chr2:40646800-40651000	Weak transcription	Ovary	ovary
15	chr2:40646800-40657800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:40647600-40649400	Enhancers	Aorta	Aorta
17	chr2:40647600-40649400	Enhancers	Right Atrium	heart
18	chr2:40647600-40662200	Weak transcription	Brain Germinal Matrix	brain
19	chr2:40647800-40649400	Enhancers	Right Ventricle	heart
20	chr2:40647800-40655600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:40647800-40658200	Weak transcription	Osteobl	bone
22	chr2:40648000-40658200	Weak transcription	Brain Anterior Caudate	brain
23	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:40648200-40649400	Enhancers	Left Ventricle	heart
25	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
26	chr2:40648400-40658200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:40648600-40649400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:40648600-40649400	Enhancers	Fetal Heart	heart
29	chr2:40648800-40649400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:40648800-40649400	Enhancers	NHLF	lung
31	chr2:40649000-40649200	Enhancers	Fetal Muscle Leg	muscle
32	chr2:40649000-40649200	Enhancers	NH-A	brain
33	chr2:40649000-40649400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:40649000-40649400	Enhancers	Pancreas	Pancrea
35	chr2:40649000-40649400	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:40649000-40649800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:40649000-40649800	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links