Variant report

Variant	rs13220495
Chromosome Location	chr6:26441640-26441641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:26439051-26443264	SK-N-SH	brain:	n/a	chr6:26440672-26440680 chr6:26440696-26440705 chr6:26440662-26440677 chr6:26439759-26439772
2	MYC	chr6:26440417-26441650	MCF10A-Er-Src	breast:	n/a	chr6:26441077-26441087
3	RFX5	chr6:26439212-26442732	IMR90	lung:	n/a	chr6:26440672-26440680 chr6:26440696-26440705 chr6:26440662-26440677 chr6:26439759-26439772
4	MXI1	chr6:26439693-26441677	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26440449..26443327-chr6:26444566..26448075,3	K562	blood:

Variant related genes	Relation type
BTN3A3	TF binding region
ENSG00000111801	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484439	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11966360	0.80[CEU][hapmap]
rs13195509	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs13198716	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs13220261	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs13220522	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2072803	1.00[YRI][hapmap]
rs2072806	1.00[YRI][hapmap]
rs2076030	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2235251	0.81[AMR][1000 genomes]
rs2393593	1.00[YRI][hapmap]
rs2393667	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs34104395	0.83[EUR][1000 genomes]
rs34107459	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34148261	0.81[EUR][1000 genomes]
rs34158769	0.89[EUR][1000 genomes]
rs34273322	0.81[AMR][1000 genomes]
rs34605993	0.81[EUR][1000 genomes]
rs35162296	0.89[EUR][1000 genomes]
rs35400317	0.84[AFR][1000 genomes]
rs35433030	0.81[EUR][1000 genomes]
rs35555795	0.81[EUR][1000 genomes]
rs35627490	0.83[EUR][1000 genomes]
rs35680819	0.83[EUR][1000 genomes]
rs35942482	0.81[AMR][1000 genomes]
rs35942569	0.87[EUR][1000 genomes]
rs36033628	0.83[EUR][1000 genomes]
rs3734542	0.83[EUR][1000 genomes]
rs3734543	0.83[EUR][1000 genomes]
rs3823158	0.83[EUR][1000 genomes]
rs41266839	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55706012	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66757203	0.83[EUR][1000 genomes]
rs66941101	0.81[EUR][1000 genomes]
rs6903015	0.91[CEU][hapmap]
rs6923139	0.91[CEU][hapmap]
rs6939978	0.90[CEU][hapmap]
rs72843784	0.92[EUR][1000 genomes]
rs9358938	1.00[YRI][hapmap]
rs9358939	0.81[AMR][1000 genomes]
rs9366656	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9379864	1.00[YRI][hapmap]
rs9379873	0.81[AMR][1000 genomes]
rs9379875	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9393718	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9467701	0.91[CEU][hapmap]
rs9467704	1.00[CEU][hapmap]
rs9467714	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs13220495	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13220495	BTN3A2	cis	Nerve Tibial	GTEx
rs13220495	BTN3A2	cis	Artery Tibial	GTEx
rs13220495	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs13220495	BTN3A2	cis	Stomach	GTEx
rs13220495	BTN3A2	cis	lung	GTEx
rs13220495	BTN3A2	cis	normal skin	skin_eQTL
rs13220495	BTN3A2	cis	Muscle Skeletal	GTEx
rs13220495	BTN3A2	cis	Esophagus Muscularis	GTEx
rs13220495	BTN3A2	cis	uninvolved skin	skin_eQTL
rs13220495	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs13220495	BTN3A2	cis	Thyroid	GTEx
rs13220495	BTN3A2	cis	Artery Aorta	GTEx
rs13220495	BTN3A2	cis	Esophagus Mucosa	GTEx
rs13220495	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs13220495	BTN3A2	cis	multi-tissue	Pritchard
rs13220495	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs13220495	BTN3A2	cis	Whole Blood	GTEx
rs13220495	BTN3A2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26439600-26443000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:26440000-26442600	Active TSS	Right Atrium	heart
3	chr6:26440000-26442600	Active TSS	NHLF	lung
4	chr6:26440200-26441800	Active TSS	Colonic Mucosa	Colon
5	chr6:26440200-26442000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:26440200-26442000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:26440200-26442000	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:26440200-26442000	Active TSS	Fetal Stomach	stomach
9	chr6:26440200-26442200	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr6:26440200-26442200	Active TSS	Fetal Muscle Leg	muscle
11	chr6:26440200-26442400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr6:26440200-26442800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:26440400-26441800	Active TSS	Primary monocytes fromperipheralblood	blood
14	chr6:26440400-26441800	Active TSS	Primary B cells from peripheral blood	blood
15	chr6:26440400-26441800	Active TSS	Fetal Thymus	thymus
16	chr6:26440400-26442000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:26440400-26442000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:26440400-26442000	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr6:26440400-26442200	Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:26440400-26442200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:26440400-26442200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr6:26440400-26442200	Active TSS	Colon Smooth Muscle	Colon
23	chr6:26440400-26442200	Active TSS	Fetal Lung	lung
24	chr6:26440400-26442400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr6:26440400-26442400	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr6:26440400-26442400	Active TSS	GM12878-XiMat	blood
27	chr6:26440400-26442600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:26440400-26442600	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr6:26441000-26442000	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr6:26441000-26442600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:26441000-26442800	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr6:26441000-26443000	Flanking Active TSS	Dnd41	blood
33	chr6:26441000-26443200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr6:26441200-26441800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:26441200-26441800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:26441200-26442200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:26441200-26442200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:26441200-26442200	Weak transcription	Left Ventricle	heart
39	chr6:26441200-26442200	Weak transcription	Lung	lung
40	chr6:26441200-26442600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:26441200-26442600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:26441200-26442600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr6:26441200-26443000	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr6:26441200-26444200	Weak transcription	Spleen	Spleen
45	chr6:26441200-26444600	Weak transcription	Gastric	stomach
46	chr6:26441200-26444600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:26441200-26444600	Weak transcription	K562	blood
48	chr6:26441200-26446400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:26441200-26449600	Weak transcription	Esophagus	oesophagus
50	chr6:26441200-26457000	Weak transcription	Brain Substantia Nigra	brain

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