Variant report

Variant	rs2393664
Chromosome Location	chr6:26460254-26460255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26457960..26461047-chr6:26519488..26522400,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199289	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10447390	0.81[CEU][hapmap]
rs10447391	0.81[CEU][hapmap]
rs10456047	0.81[CEU][hapmap]
rs10456331	0.81[CEU][hapmap]
rs10484441	0.81[CEU][hapmap]
rs10484443	1.00[JPT][hapmap]
rs10807008	0.81[CEU][hapmap]
rs10946820	0.81[CEU][hapmap]
rs10946821	0.81[CEU][hapmap]
rs10946823	0.86[CEU][hapmap]
rs10946824	0.80[CEU][hapmap]
rs10946826	0.80[CEU][hapmap]
rs10946829	0.80[CEU][hapmap]
rs10946832	0.81[CEU][hapmap]
rs1131936	0.87[CEU][hapmap]
rs12191917	0.80[CEU][hapmap]
rs12193283	0.81[CEU][hapmap]
rs12194001	0.83[CEU][hapmap]
rs12194036	0.81[CEU][hapmap]
rs12194073	0.81[CEU][hapmap]
rs12196371	0.81[CEU][hapmap]
rs12198993	0.81[CEU][hapmap]
rs12201546	0.80[CEU][hapmap]
rs12206812	0.80[CEU][hapmap]
rs12207930	0.80[CEU][hapmap]
rs12208211	0.81[CEU][hapmap]
rs12208788	0.87[CEU][hapmap]
rs12211872	0.81[CEU][hapmap]
rs12214444	0.81[CEU][hapmap]
rs12214486	0.81[CEU][hapmap]
rs12214924	0.80[CEU][hapmap]
rs12661560	0.81[CEU][hapmap]
rs12664899	0.87[CEU][hapmap]
rs16891790	1.00[JPT][hapmap]
rs17537465	0.87[CEU][hapmap]
rs17539219	0.80[CEU][hapmap]
rs17610161	0.81[CEU][hapmap]
rs17611220	0.81[CEU][hapmap]
rs1884945	0.81[CEU][hapmap]
rs2273193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2273558	0.84[CHB][hapmap]
rs2393652	0.80[CEU][hapmap]
rs2893845	0.80[CEU][hapmap]
rs2893847	0.80[CEU][hapmap]
rs2893848	0.80[CEU][hapmap]
rs2893849	0.87[CEU][hapmap]
rs2893856	0.87[CEU][hapmap]
rs2893857	0.81[CEU][hapmap]
rs3846843	0.80[CEU][hapmap]
rs3846844	0.81[CEU][hapmap]
rs3846847	0.81[CEU][hapmap]
rs3846848	0.80[CEU][hapmap]
rs3846849	0.81[CEU][hapmap]
rs3902051	0.87[CEU][hapmap]
rs4083469	0.81[CEU][hapmap]
rs4609015	0.80[CEU][hapmap]
rs4711109	0.81[CEU][hapmap]
rs4711111	0.81[CEU][hapmap]
rs4712986	0.87[CEU][hapmap]
rs4712988	0.87[CEU][hapmap]
rs4712990	0.81[CEU][hapmap]
rs4712993	0.80[CEU][hapmap]
rs4712994	0.80[CEU][hapmap]
rs4712996	0.80[CEU][hapmap]
rs4712998	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712999	0.86[CEU][hapmap]
rs4713001	0.81[CEU][hapmap]
rs6456723	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6456724	0.87[CEU][hapmap]
rs6900725	0.80[CEU][hapmap]
rs6910023	0.81[CEU][hapmap]
rs6911765	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6912934	0.87[CEU][hapmap]
rs6920986	0.80[CEU][hapmap]
rs6926878	0.80[CEU][hapmap]
rs6928454	0.81[CEU][hapmap]
rs6929846	0.93[CEU][hapmap]
rs7355	0.87[CEU][hapmap]
rs7356849	0.87[CEU][hapmap]
rs7356982	0.81[CEU][hapmap]
rs7744254	0.80[CEU][hapmap]
rs7745238	0.81[CEU][hapmap]
rs7745767	0.81[CEU][hapmap]
rs7751280	0.80[CEU][hapmap]
rs7768108	0.81[CEU][hapmap]
rs7770214	0.80[CEU][hapmap]
rs882010	0.81[CEU][hapmap]
rs9295690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348718	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs9348727	0.91[JPT][hapmap]
rs9358942	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393721	0.82[JPT][hapmap]
rs9393722	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9467759	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	esv2763996	chr6:26423901-26465384	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1017824	chr6:26425410-26465384	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1030289	chr6:26428314-26464017	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1033003	chr6:26428314-26465384	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv1031229	chr6:26428314-26467182	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1031238	chr6:26428314-26471596	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1024483	chr6:26429262-26465384	Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv1034561	chr6:26429262-26467182	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv528172	chr6:26430981-26463660	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
16	nsv1029357	chr6:26432815-26464789	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
17	nsv1023581	chr6:26432815-26465384	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
18	nsv1024222	chr6:26432815-26467182	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1022309	chr6:26434914-26464789	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv601185	chr6:26455811-26465384	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
21	nsv965689	chr6:26457033-26469487	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2393664	BTN2A1	cis	Whole Blood	GTEx
rs2393664	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26457600-26460400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:26459000-26463400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:26459200-26461200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr6:26459200-26461600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:26459200-26461600	Genic enhancers	Fetal Muscle Leg	muscle
6	chr6:26459200-26462000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:26459200-26462800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:26459200-26463000	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr6:26459200-26463000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:26459200-26463800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:26459200-26463800	Genic enhancers	Spleen	Spleen
12	chr6:26459400-26460400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
13	chr6:26459400-26460400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:26459400-26460400	Genic enhancers	Ovary	ovary
15	chr6:26459400-26460400	Genic enhancers	Pancreas	Pancrea
16	chr6:26459400-26460400	Transcr. at gene 5' and 3'	NHLF	lung
17	chr6:26459400-26460600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
18	chr6:26459400-26460600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
19	chr6:26459400-26460600	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr6:26459400-26460800	Enhancers	Small Intestine	intestine
21	chr6:26459400-26461400	Genic enhancers	Fetal Thymus	thymus
22	chr6:26459400-26461400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
23	chr6:26459400-26461600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:26459400-26461600	Genic enhancers	Brain Substantia Nigra	brain
25	chr6:26459400-26461600	Genic enhancers	Fetal Lung	lung
26	chr6:26459400-26461600	Genic enhancers	Fetal Stomach	stomach
27	chr6:26459400-26461600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:26459400-26461800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
29	chr6:26459400-26462000	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr6:26459600-26460400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:26459600-26460400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:26459600-26460400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:26459600-26460400	Enhancers	Fetal Heart	heart
34	chr6:26459600-26460400	Genic enhancers	Gastric	stomach
35	chr6:26459600-26460400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
36	chr6:26459600-26460400	Genic enhancers	K562	blood
37	chr6:26459600-26460600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:26459600-26461200	Genic enhancers	Osteobl	bone
39	chr6:26459600-26461400	Genic enhancers	HUVEC	blood vessel
40	chr6:26459600-26461600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:26459600-26461600	Genic enhancers	Liver	Liver
42	chr6:26459600-26461600	Genic enhancers	Brain Anterior Caudate	brain
43	chr6:26459600-26461600	Genic enhancers	Brain Hippocampus Middle	brain
44	chr6:26459600-26461600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
45	chr6:26459600-26461600	Genic enhancers	Fetal Intestine Large	intestine
46	chr6:26459600-26461600	Genic enhancers	Fetal Intestine Small	intestine
47	chr6:26459600-26461600	Genic enhancers	Left Ventricle	heart
48	chr6:26459600-26461600	Enhancers	Stomach Mucosa	stomach
49	chr6:26459600-26461600	Genic enhancers	Thymus	Thymus
50	chr6:26459600-26461600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links