Variant report

Variant	rs2754262
Chromosome Location	chr6:88405585-88405586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88298892..88302050-chr6:88403623..88406775,3	MCF-7	breast:
2	chr6:88355100..88357756-chr6:88404547..88407101,2	K562	blood:
3	chr6:88397600..88401322-chr6:88403736..88407504,4	K562	blood:
4	chr6:88391827..88396132-chr6:88405533..88410317,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135336	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:76)

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];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs13193380	0.88[EUR][1000 genomes]
rs13194003	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2246113	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300906	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2300909	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2307379	0.94[EUR][1000 genomes]
rs2325064	0.82[EUR][1000 genomes]
rs2754245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap]
rs2754247	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754248	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754260	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2754264	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2787893	0.96[CEU][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2787921	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787924	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2787927	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]
rs2787934	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2814712	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757368	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs3934838	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs4334949	0.96[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4464759	0.92[CEU][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4498321	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4587138	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587143	0.96[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs4706294	0.92[EUR][1000 genomes]
rs4707373	0.82[EUR][1000 genomes]
rs4707374	0.87[EUR][1000 genomes]
rs4707376	0.89[EUR][1000 genomes]
rs4707377	0.89[EUR][1000 genomes]
rs4707379	0.89[EUR][1000 genomes]
rs4707382	0.92[EUR][1000 genomes]
rs4707383	0.92[EUR][1000 genomes]
rs6454631	0.85[JPT][hapmap]
rs6454632	0.85[EUR][1000 genomes]
rs6454636	0.92[EUR][1000 genomes]
rs6454638	0.92[EUR][1000 genomes]
rs6454640	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6454641	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6906769	0.85[EUR][1000 genomes]
rs6908386	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6916732	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs6918909	0.82[EUR][1000 genomes]
rs6928160	0.86[EUR][1000 genomes]
rs6930600	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6931069	0.94[EUR][1000 genomes]
rs6940150	0.89[EUR][1000 genomes]
rs7741825	0.82[JPT][hapmap]
rs7742965	0.88[EUR][1000 genomes]
rs7746465	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7750207	0.89[EUR][1000 genomes]
rs7755167	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7757636	0.87[EUR][1000 genomes]
rs7757794	0.86[EUR][1000 genomes]
rs7762864	0.85[EUR][1000 genomes]
rs7772561	0.92[EUR][1000 genomes]
rs7773906	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9444512	0.82[EUR][1000 genomes]
rs9444519	0.96[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs9444522	0.87[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs9444524	0.89[EUR][1000 genomes]
rs9444525	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9444526	0.92[EUR][1000 genomes]
rs9450723	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9450732	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9450733	0.85[EUR][1000 genomes]
rs9450738	0.89[EUR][1000 genomes]
rs9450739	0.89[EUR][1000 genomes]
rs9450744	0.89[EUR][1000 genomes]
rs9450752	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs9450755	0.89[EUR][1000 genomes]
rs9450762	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs985764	0.96[CEU][hapmap];0.85[JPT][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	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
rs2754262	GJB7	cis	cerebellum	SCAN
rs2754262	C6orf162	cis	cerebellum	SCAN
rs2754262	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2754262	SLC35A1	cis	lymphoblastoid	seeQTL
rs2754262	C6orf162	cis	parietal	SCAN
rs2754262	SNORD50A	cis	cerebellum	SCAN
rs2754262	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2754262	SLC35A1	cis	multi-tissue	Pritchard
rs2754262	C6orf164	cis	Thyroid	GTEx
rs2754262	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2754262	SLC35A1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
3	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
5	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
10	chr6:88392600-88406800	Weak transcription	HSMM	muscle
11	chr6:88392600-88407200	Weak transcription	HMEC	breast
12	chr6:88393800-88405600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:88395000-88407200	Weak transcription	Hela-S3	cervix
14	chr6:88397600-88407000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:88399000-88407400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:88399600-88407400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:88399600-88408200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:88400000-88405600	Weak transcription	Fetal Intestine Small	intestine
19	chr6:88400200-88406800	Weak transcription	NH-A	brain
20	chr6:88400800-88405600	Weak transcription	Gastric	stomach
21	chr6:88400800-88410000	Weak transcription	Lung	lung
22	chr6:88401000-88408800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:88401200-88406600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:88401800-88405600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:88401800-88406600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:88402000-88406800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr6:88402000-88406800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:88402000-88407400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:88402200-88405600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:88402200-88405600	Weak transcription	Fetal Thymus	thymus
31	chr6:88402200-88405600	Weak transcription	Ovary	ovary
32	chr6:88402200-88405600	Weak transcription	Pancreas	Pancrea
33	chr6:88402200-88405800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:88402200-88406000	Weak transcription	Small Intestine	intestine
35	chr6:88402200-88406000	Weak transcription	Spleen	Spleen
36	chr6:88402200-88406400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:88402200-88406800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:88402200-88406800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:88402200-88406800	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:88402200-88407200	Weak transcription	K562	blood
41	chr6:88402200-88407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:88402200-88407800	Weak transcription	Placenta	Placenta
43	chr6:88402200-88410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:88402600-88407200	Enhancers	Adipose Nuclei	Adipose
45	chr6:88402800-88405600	Weak transcription	Right Atrium	heart
46	chr6:88402800-88407200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:88403000-88405600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:88403000-88405600	Enhancers	A549	lung
49	chr6:88403200-88406200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr6:88403200-88407800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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