Variant report

Variant	rs2325064
Chromosome Location	chr6:88224467-88224468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88222890..88225821-chr6:88239484..88241422,2	MCF-7	breast:
2	chr6:88223450..88226414-chr6:88409744..88412140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1051131	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051148	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10755484	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13193380	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13194003	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2207146	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2268993	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2268994	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2273129	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2284908	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2300906	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300909	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307379	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754247	0.85[EUR][1000 genomes]
rs2754248	0.83[EUR][1000 genomes]
rs2754260	0.82[EUR][1000 genomes]
rs2754262	0.82[EUR][1000 genomes]
rs2787893	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2787921	0.83[EUR][1000 genomes]
rs2787924	0.82[EUR][1000 genomes]
rs2814712	0.83[EUR][1000 genomes]
rs3757368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934838	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4334949	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4464759	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4498321	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4587138	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4587143	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4706294	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707373	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707374	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707376	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707377	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707379	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707382	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707383	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454631	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454632	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6454636	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454638	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454640	0.85[EUR][1000 genomes]
rs6454641	0.85[EUR][1000 genomes]
rs6906769	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6908386	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6916732	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6918909	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923230	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923355	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6928160	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930600	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6931069	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940150	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7741825	0.81[ASN][1000 genomes]
rs7742965	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7746465	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7750207	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7754350	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755167	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757636	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7757794	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7761814	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7762864	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772561	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7773906	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444504	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9444512	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444519	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444522	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444524	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444525	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444526	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450704	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450712	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9450723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450726	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450732	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450733	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450738	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450739	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450744	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450752	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450755	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450762	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs985764	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2325064	SLC35A1	cis	multi-tissue	Pritchard
rs2325064	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2325064	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2325064	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88226000	Weak transcription	Gastric	stomach
2	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
3	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
4	chr6:88191200-88227400	Weak transcription	Spleen	Spleen
5	chr6:88193600-88227600	Weak transcription	Pancreas	Pancrea
6	chr6:88193800-88227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:88194000-88226200	Weak transcription	Lung	lung
8	chr6:88194000-88249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:88194600-88228200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:88200600-88227400	Weak transcription	Small Intestine	intestine
11	chr6:88205200-88224600	Weak transcription	Stomach Mucosa	stomach
12	chr6:88207200-88242600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:88210200-88231400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:88210200-88232800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:88210200-88240600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:88210400-88235000	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr6:88210800-88224600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:88210800-88224600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr6:88210800-88230800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:88210800-88230800	Strong transcription	Fetal Thymus	thymus
21	chr6:88210800-88231400	Strong transcription	Osteobl	bone
22	chr6:88210800-88235000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:88211000-88231400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:88211000-88235000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:88211000-88235200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:88211000-88241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:88211200-88230800	Strong transcription	Liver	Liver
28	chr6:88211800-88224600	Strong transcription	HUVEC	blood vessel
29	chr6:88212000-88245200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:88212800-88227400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:88213000-88224600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:88213000-88225400	Weak transcription	Brain Substantia Nigra	brain
33	chr6:88213000-88226200	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:88213400-88227200	Weak transcription	Psoas Muscle	Psoas
35	chr6:88213400-88227400	Weak transcription	Esophagus	oesophagus
36	chr6:88214000-88231400	Strong transcription	NH-A	brain
37	chr6:88214200-88224800	Strong transcription	Primary T cells from cord blood	blood
38	chr6:88214200-88231400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr6:88214200-88244400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:88214600-88226200	Weak transcription	Fetal Heart	heart
41	chr6:88214800-88235400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:88215000-88226000	Weak transcription	HSMMtube	muscle
43	chr6:88215000-88231400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:88215200-88235000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:88215200-88235000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:88215800-88240800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:88216200-88225000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:88216200-88231800	Strong transcription	HSMM	muscle
49	chr6:88217400-88226000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:88217400-88232800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links