Variant report

Variant	rs9357006
Chromosome Location	chr6:26364628-26364629
allele	A/C
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	chr6:26364506-26366305	K562	blood:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
2	MXI1	chr6:26364117-26367241	SK-N-SH	brain:	n/a	chr6:26365782-26365791
3	RFX5	chr6:26362983-26367827	IMR90	lung:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
4	RFX5	chr6:26364327-26366044	H1-hESC	embryonic stem cell:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
5	WRNIP1	chr6:26364413-26364715	GM12878	blood:	n/a	n/a
6	MAX	chr6:26364387-26364741	NB4	blood:	n/a	n/a
7	RFX5	chr6:26362934-26367943	SK-N-SH	brain:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
8	IRF1	chr6:26364536-26366099	K562	blood:	n/a	chr6:26365322-26365336 chr6:26365325-26365337 chr6:26365462-26365473 chr6:26365324-26365335 chr6:26365326-26365336 chr6:26365325-26365339 chr6:26365326-26365340 chr6:26365464-26365474 chr6:26365324-26365344 chr6:26365320-26365341 chr6:26365460-26365474 chr6:26365325-26365336 chr6:26365325-26365337 chr6:26365464-26365478
9	RFX5	chr6:26364309-26366049	Hela-S3	cervix:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375
10	RUNX3	chr6:26364458-26364900	GM12878	blood:	n/a	n/a
11	MYC	chr6:26364359-26364809	NB4	blood:	n/a	n/a
12	RFX5	chr6:26364566-26365942	HepG2	liver:	n/a	chr6:26365394-26365403 chr6:26365363-26365372 chr6:26365370-26365378 chr6:26365360-26365375

No.	Distal block	Cell Line	Cell type
1	chr6:26361226..26362867-chr6:26363183..26365320,2	MCF-7	breast:
2	chr6:26363140..26366680-chr6:26382117..26385194,3	MCF-7	breast:
3	chr6:26360935..26366570-chr6:26520779..26523276,5	K562	blood:
4	chr6:26196455..26200961-chr6:26360873..26365378,4	K562	blood:
5	chr6:26341478..26343917-chr6:26362438..26365038,2	K562	blood:

Variant related genes	Relation type
BTN3A2	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000124508	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs12173854	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174602	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174623	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174631	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174639	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12176317	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13191660	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13216828	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16891725	0.82[EUR][1000 genomes]
rs1977	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1978	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1979	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2072803	0.88[EUR][1000 genomes]
rs2072806	0.88[EUR][1000 genomes]
rs2073527	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073529	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073530	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073531	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076030	0.88[EUR][1000 genomes]
rs2235251	0.87[EUR][1000 genomes]
rs2393667	0.87[EUR][1000 genomes]
rs28362606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551159	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3047288	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34273322	0.87[EUR][1000 genomes]
rs34436535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34550936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34622023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35304979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35307327	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35934643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35942482	0.87[EUR][1000 genomes]
rs3757138	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58825580	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66823108	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66827971	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67509210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68072215	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs68112369	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900665	0.88[EUR][1000 genomes]
rs71544290	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71557332	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71557334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71557335	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841536	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9348709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348716	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348721	0.88[EUR][1000 genomes]
rs9358930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358935	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358937	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358938	0.88[EUR][1000 genomes]
rs9358939	0.87[EUR][1000 genomes]
rs9366653	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366654	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9366655	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9366656	0.87[EUR][1000 genomes]
rs9379850	0.92[ASN][1000 genomes]
rs9379851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379857	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379858	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379863	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379864	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379871	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379873	0.90[EUR][1000 genomes]
rs9379875	0.87[EUR][1000 genomes]
rs9393703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393710	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393711	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393713	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393714	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393715	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393718	0.88[EUR][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	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9357006	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9357006	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs9357006	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9357006	BTN3A2	cis	Nerve Tibial	GTEx
rs9357006	BTN3A2	cis	lung	GTEx
rs9357006	BTN3A2	cis	Stomach	GTEx
rs9357006	BTN3A2	cis	Artery Tibial	GTEx
rs9357006	BTN3A2	cis	Thyroid	GTEx
rs9357006	BTN3A2	cis	Artery Aorta	GTEx
rs9357006	BTN3A2	cis	Esophagus Mucosa	GTEx
rs9357006	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9357006	BTN3A2	cis	Heart Left Ventricle	GTEx
rs9357006	BTN3A2	cis	Whole Blood	GTEx
rs9357006	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs9357006	BTN3A2	cis	Muscle Skeletal	GTEx
rs9357006	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26356200-26365400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:26363400-26365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:26364000-26364800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:26364200-26364800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:26364200-26364800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:26364200-26364800	Enhancers	Esophagus	oesophagus
7	chr6:26364200-26364800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:26364200-26364800	Enhancers	Fetal Intestine Large	intestine
9	chr6:26364200-26364800	Enhancers	Fetal Muscle Trunk	muscle
10	chr6:26364200-26364800	Enhancers	Placenta	Placenta
11	chr6:26364200-26364800	Enhancers	Fetal Stomach	stomach
12	chr6:26364200-26364800	Enhancers	Gastric	stomach
13	chr6:26364200-26364800	Enhancers	Pancreas	Pancrea
14	chr6:26364200-26364800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:26364200-26364800	Enhancers	Small Intestine	intestine
16	chr6:26364200-26364800	Enhancers	Spleen	Spleen
17	chr6:26364200-26364800	Flanking Active TSS	K562	blood
18	chr6:26364200-26365000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr6:26364200-26365000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:26364200-26365000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr6:26364200-26365000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:26364200-26365000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:26364200-26365000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:26364200-26365000	Enhancers	Left Ventricle	heart
25	chr6:26364200-26365000	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr6:26364200-26365200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:26364200-26365200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr6:26364200-26365200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr6:26364200-26365200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:26364200-26365200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:26364200-26365200	Flanking Active TSS	Dnd41	blood
32	chr6:26364200-26366000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:26364400-26364800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr6:26364400-26364800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:26364400-26364800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:26364400-26364800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:26364400-26364800	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr6:26364400-26364800	Enhancers	Colonic Mucosa	Colon
39	chr6:26364400-26364800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr6:26364400-26364800	Flanking Active TSS	Psoas Muscle	Psoas
41	chr6:26364400-26364800	Flanking Active TSS	A549	lung
42	chr6:26364400-26365000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:26364400-26365000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:26364400-26365000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr6:26364400-26365000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:26364400-26365000	Flanking Active TSS	Liver	Liver
47	chr6:26364400-26365000	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr6:26364400-26365000	Enhancers	Brain Germinal Matrix	brain
49	chr6:26364400-26365000	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr6:26364400-26365000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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