Variant report

Variant	rs56023587
Chromosome Location	chr6:26402614-26402615
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26400774..26405587-chr6:26406042..26409897,8	K562	blood:
2	chr6:26390074..26392884-chr6:26401508..26403224,2	K562	blood:
3	chr6:26400255..26403237-chr6:26521906..26524697,3	K562	blood:
4	chr6:26157049..26158999-chr6:26401561..26403598,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTN2A2-1	chr6:26402478-26402640	NONHSAT108276

Variant related genes	Relation type
ENSG00000026950	Chromatin interaction
ENSG00000124508	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10447390	1.00[ASN][1000 genomes]
rs10447391	1.00[ASN][1000 genomes]
rs10807008	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946820	1.00[ASN][1000 genomes]
rs10946821	1.00[ASN][1000 genomes]
rs10946823	1.00[ASN][1000 genomes]
rs10946824	1.00[ASN][1000 genomes]
rs10946825	1.00[ASN][1000 genomes]
rs10946826	1.00[ASN][1000 genomes]
rs10946827	1.00[ASN][1000 genomes]
rs10946828	1.00[ASN][1000 genomes]
rs10946829	1.00[ASN][1000 genomes]
rs10946830	1.00[ASN][1000 genomes]
rs10946832	1.00[ASN][1000 genomes]
rs1131936	0.91[EUR][1000 genomes]
rs12191917	1.00[ASN][1000 genomes]
rs12194001	1.00[ASN][1000 genomes]
rs12194073	1.00[ASN][1000 genomes]
rs12194412	1.00[ASN][1000 genomes]
rs12196371	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198993	1.00[ASN][1000 genomes]
rs12201546	1.00[ASN][1000 genomes]
rs12203108	1.00[ASN][1000 genomes]
rs12203120	1.00[ASN][1000 genomes]
rs12205476	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12206812	1.00[ASN][1000 genomes]
rs12206839	1.00[ASN][1000 genomes]
rs12207930	1.00[ASN][1000 genomes]
rs12208329	1.00[ASN][1000 genomes]
rs12208788	0.91[EUR][1000 genomes]
rs12213625	1.00[ASN][1000 genomes]
rs12214444	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214486	1.00[ASN][1000 genomes]
rs12214924	1.00[ASN][1000 genomes]
rs12214976	1.00[ASN][1000 genomes]
rs12662604	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664899	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17537465	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17539219	1.00[ASN][1000 genomes]
rs17610161	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17611220	1.00[ASN][1000 genomes]
rs2393652	0.92[ASN][1000 genomes]
rs2393655	1.00[ASN][1000 genomes]
rs2393656	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571747	1.00[ASN][1000 genomes]
rs2893844	1.00[ASN][1000 genomes]
rs2893845	1.00[ASN][1000 genomes]
rs2893846	1.00[ASN][1000 genomes]
rs2893847	1.00[ASN][1000 genomes]
rs2893848	1.00[ASN][1000 genomes]
rs3198487	1.00[ASN][1000 genomes]
rs3208734	1.00[ASN][1000 genomes]
rs34268421	1.00[ASN][1000 genomes]
rs3807025	1.00[ASN][1000 genomes]
rs3846843	1.00[ASN][1000 genomes]
rs3846844	1.00[ASN][1000 genomes]
rs3846847	1.00[ASN][1000 genomes]
rs3846848	1.00[ASN][1000 genomes]
rs3846849	1.00[ASN][1000 genomes]
rs3902051	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903661	1.00[ASN][1000 genomes]
rs4083469	1.00[ASN][1000 genomes]
rs41266835	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4305717	1.00[ASN][1000 genomes]
rs45499696	1.00[ASN][1000 genomes]
rs4609015	1.00[ASN][1000 genomes]
rs4711108	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711109	1.00[ASN][1000 genomes]
rs4711110	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711111	1.00[ASN][1000 genomes]
rs4712986	0.91[EUR][1000 genomes]
rs4712989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712990	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712992	1.00[ASN][1000 genomes]
rs4712993	1.00[ASN][1000 genomes]
rs4712994	1.00[ASN][1000 genomes]
rs4712995	1.00[ASN][1000 genomes]
rs4712996	1.00[ASN][1000 genomes]
rs55775018	1.00[ASN][1000 genomes]
rs55786210	1.00[ASN][1000 genomes]
rs55957716	1.00[ASN][1000 genomes]
rs55994013	1.00[ASN][1000 genomes]
rs56143200	1.00[ASN][1000 genomes]
rs56157336	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161420	1.00[ASN][1000 genomes]
rs56182232	1.00[ASN][1000 genomes]
rs56190518	1.00[ASN][1000 genomes]
rs56207464	1.00[ASN][1000 genomes]
rs56280732	1.00[ASN][1000 genomes]
rs56325223	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57275245	1.00[ASN][1000 genomes]
rs60750900	1.00[ASN][1000 genomes]
rs6456721	1.00[ASN][1000 genomes]
rs6456722	1.00[ASN][1000 genomes]
rs6900725	1.00[ASN][1000 genomes]
rs6901245	1.00[ASN][1000 genomes]
rs6910023	1.00[ASN][1000 genomes]
rs6920986	1.00[ASN][1000 genomes]
rs6926878	1.00[ASN][1000 genomes]
rs6928454	1.00[ASN][1000 genomes]
rs6931648	1.00[ASN][1000 genomes]
rs72841540	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7355	0.91[EUR][1000 genomes]
rs7356849	0.91[EUR][1000 genomes]
rs7744254	1.00[ASN][1000 genomes]
rs7745238	1.00[ASN][1000 genomes]
rs7745767	1.00[ASN][1000 genomes]
rs7751280	1.00[ASN][1000 genomes]
rs7754940	1.00[ASN][1000 genomes]
rs7755398	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768108	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770214	1.00[ASN][1000 genomes]
rs7770699	1.00[ASN][1000 genomes]
rs7775365	1.00[ASN][1000 genomes]
rs9461245	0.82[AFR][1000 genomes]
rs9467750	0.91[EUR][1000 genomes]
rs9467751	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv883491	chr6:26367689-26410800	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv883492	chr6:26367689-26436592	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv883493	chr6:26367689-26442786	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv883494	chr6:26367833-26442786	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv883495	chr6:26367833-26443853	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3334611	chr6:26367893-26443308	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	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
13	nsv883496	chr6:26369549-26413088	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv883497	chr6:26369549-26442786	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv883498	chr6:26369549-26443853	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1030863	chr6:26371006-26405990	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv883499	chr6:26377591-26454454	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
18	esv3427999	chr6:26378373-26453532	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv462664	chr6:26379537-26451553	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv601184	chr6:26379537-26451553	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56023587	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs56023587	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs56023587	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26394000-26412000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26401400-26403200	Active TSS	Brain Angular Gyrus	brain
3	chr6:26401400-26403600	Active TSS	Psoas Muscle	Psoas
4	chr6:26401800-26402800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:26401800-26402800	Active TSS	Muscle Satellite Cultured Cells	--
6	chr6:26401800-26402800	Active TSS	Liver	Liver
7	chr6:26401800-26402800	Active TSS	HSMM	muscle
8	chr6:26401800-26403000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:26401800-26403000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr6:26401800-26403000	Active TSS	Rectal Smooth Muscle	rectum
11	chr6:26401800-26403000	Active TSS	A549	lung
12	chr6:26401800-26403200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:26401800-26403200	Active TSS	Brain Anterior Caudate	brain
14	chr6:26401800-26403200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr6:26401800-26403200	Active TSS	Brain Substantia Nigra	brain
16	chr6:26401800-26403200	Active TSS	Colon Smooth Muscle	Colon
17	chr6:26401800-26403200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr6:26401800-26403200	Active TSS	HMEC	breast
19	chr6:26401800-26403400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:26401800-26403400	Active TSS	Brain Germinal Matrix	brain
21	chr6:26401800-26403600	Active TSS	Brain Hippocampus Middle	brain
22	chr6:26401800-26403600	Active TSS	Stomach Smooth Muscle	stomach
23	chr6:26401800-26404600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:26401800-26404800	Weak transcription	Spleen	Spleen
25	chr6:26402000-26402800	Active TSS	Duodenum Mucosa	Duodenum
26	chr6:26402000-26402800	Active TSS	Fetal Heart	heart
27	chr6:26402000-26403000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr6:26402000-26403000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:26402000-26403000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:26402000-26403000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:26402000-26403000	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr6:26402000-26403000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:26402000-26403000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:26402000-26403000	Active TSS	Aorta	Aorta
35	chr6:26402000-26403000	Active TSS	Brain Cingulate Gyrus	brain
36	chr6:26402000-26403000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:26402000-26403000	Active TSS	Left Ventricle	heart
38	chr6:26402000-26403000	Active TSS	Right Ventricle	heart
39	chr6:26402000-26403000	Active TSS	Stomach Mucosa	stomach
40	chr6:26402000-26403200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr6:26402000-26403200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr6:26402000-26403200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr6:26402000-26403200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:26402000-26403200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr6:26402000-26403200	Active TSS	Fetal Muscle Leg	muscle
46	chr6:26402000-26403200	Active TSS	Ovary	ovary
47	chr6:26402000-26403200	Active TSS	Right Atrium	heart
48	chr6:26402000-26403200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr6:26402000-26403200	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr6:26402000-26403400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links