Variant report

Variant	rs2787927
Chromosome Location	chr6:88412786-88412787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1051131	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs1051148	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs10755484	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]
rs13193380	0.82[EUR][1000 genomes]
rs13194003	0.86[EUR][1000 genomes]
rs2246113	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307379	0.88[EUR][1000 genomes]
rs2754245	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap]
rs2754247	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2754248	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2754260	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754262	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2754264	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787893	0.96[CEU][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2787921	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2787924	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2787930	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2787934	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2814712	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757368	0.96[CEU][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]
rs3934838	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs4334949	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4464759	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs4498321	0.86[EUR][1000 genomes]
rs4587138	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs4587143	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs4706294	0.86[EUR][1000 genomes]
rs4707374	0.81[EUR][1000 genomes]
rs4707376	0.83[EUR][1000 genomes]
rs4707377	0.83[EUR][1000 genomes]
rs4707379	0.83[EUR][1000 genomes]
rs4707382	0.86[EUR][1000 genomes]
rs4707383	0.86[EUR][1000 genomes]
rs6454631	0.85[JPT][hapmap]
rs6454636	0.86[EUR][1000 genomes]
rs6454638	0.86[EUR][1000 genomes]
rs6454640	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6454641	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6908386	0.86[EUR][1000 genomes]
rs6916732	0.96[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs6928160	0.80[EUR][1000 genomes]
rs6930600	0.86[EUR][1000 genomes]
rs6931069	0.88[EUR][1000 genomes]
rs6940150	0.83[EUR][1000 genomes]
rs7741825	0.82[JPT][hapmap]
rs7742965	0.82[EUR][1000 genomes]
rs7746465	0.86[EUR][1000 genomes]
rs7750207	0.83[EUR][1000 genomes]
rs7755167	0.86[EUR][1000 genomes]
rs7757636	0.81[EUR][1000 genomes]
rs7757794	0.80[EUR][1000 genomes]
rs7772561	0.86[EUR][1000 genomes]
rs7773906	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs9444519	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs9444522	0.87[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs9444524	0.83[EUR][1000 genomes]
rs9444525	0.85[EUR][1000 genomes]
rs9444526	0.86[EUR][1000 genomes]
rs9450723	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs9450732	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs9450738	0.83[EUR][1000 genomes]
rs9450739	0.83[EUR][1000 genomes]
rs9450744	0.83[EUR][1000 genomes]
rs9450752	0.92[CEU][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs9450755	0.83[EUR][1000 genomes]
rs9450762	0.85[EUR][1000 genomes]
rs985764	0.96[CEU][hapmap];0.85[JPT][hapmap]

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	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv7941	chr6:88403555-88413595	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2787927	C6orf162	cis	parietal	SCAN
rs2787927	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2787927	GJB7	cis	cerebellum	SCAN
rs2787927	SLC35A1	cis	parietal	SCAN
rs2787927	C6orf164	cis	Thyroid	GTEx
rs2787927	SLC35A1	cis	multi-tissue	Pritchard
rs2787927	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2787927	SLC35A1	cis	lymphoblastoid	seeQTL
rs2787927	SNORD50A	cis	cerebellum	SCAN
rs2787927	C6orf162	cis	cerebellum	SCAN
rs2787927	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88407000-88412800	Active TSS	Thymus	Thymus
2	chr6:88407400-88412800	Active TSS	Aorta	Aorta
3	chr6:88407400-88413200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:88407400-88413200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:88407400-88413200	Active TSS	Psoas Muscle	Psoas
6	chr6:88407600-88412800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr6:88407600-88413000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:88407600-88413000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:88407600-88413000	Active TSS	HSMMtube	muscle
10	chr6:88407800-88412800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:88408000-88412800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:88408000-88412800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:88408000-88412800	Active TSS	Fetal Intestine Large	intestine
14	chr6:88408000-88412800	Active TSS	Fetal Intestine Small	intestine
15	chr6:88408000-88412800	Active TSS	Fetal Muscle Leg	muscle
16	chr6:88408000-88413000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:88408000-88413000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:88408000-88413000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:88408000-88413000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr6:88408000-88413000	Active TSS	Stomach Smooth Muscle	stomach
21	chr6:88408000-88413000	Active TSS	HMEC	breast
22	chr6:88408000-88413000	Active TSS	HSMM	muscle
23	chr6:88408000-88413000	Active TSS	NHDF-Ad	bronchial
24	chr6:88408000-88413200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:88408200-88412800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr6:88408200-88412800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:88408200-88412800	Active TSS	Placenta	Placenta
28	chr6:88408200-88413000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr6:88408200-88413000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:88408200-88413000	Active TSS	NHLF	lung
31	chr6:88408200-88413200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:88408200-88413200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:88408400-88412800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:88408400-88412800	Active TSS	Fetal Stomach	stomach
35	chr6:88408400-88412800	Active TSS	Fetal Thymus	thymus
36	chr6:88408400-88412800	Active TSS	Right Ventricle	heart
37	chr6:88408400-88413000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:88408400-88413000	Active TSS	Fetal Kidney	kidney
39	chr6:88408400-88413000	Active TSS	Rectal Smooth Muscle	rectum
40	chr6:88408400-88413000	Active TSS	NHEK	skin
41	chr6:88408400-88413200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:88408400-88413200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:88408600-88412800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:88408600-88413000	Active TSS	Brain Anterior Caudate	brain
45	chr6:88408600-88413200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:88408800-88412800	Active TSS	Muscle Satellite Cultured Cells	--
47	chr6:88408800-88412800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:88409400-88413000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr6:88409600-88412800	Active TSS	Brain Substantia Nigra	brain
50	chr6:88409800-88413000	Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links