Variant report

Variant	rs17598658
Chromosome Location	chr6:26175866-26175867
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26174601..26176102-chr6:26570982..26573796,2	K562	blood:
2	chr6:26173162..26176742-chr6:26593702..26596489,3	K562	blood:
3	chr6:26175802..26177395-chr6:27113078..27114655,2	MCF-7	breast:
4	chr6:26175369..26176431-chr6:26595705..26596639,4	K562	blood:
5	chr6:26175039..26176164-chr6:26188820..26189580,3	K562	blood:
6	chr6:26175686..26176293-chr6:26217119..26217888,3	K562	blood:

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000168274	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484439	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11966360	0.80[CEU][hapmap]
rs13191445	0.81[CEU][hapmap]
rs13202688	0.81[CEU][hapmap]
rs13204572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13212534	0.89[CEU][hapmap]
rs13220522	0.81[EUR][1000 genomes]
rs2393593	1.00[YRI][hapmap]
rs34107459	0.81[EUR][1000 genomes]
rs34158769	0.81[EUR][1000 genomes]
rs34961555	0.98[EUR][1000 genomes]
rs35162296	0.81[EUR][1000 genomes]
rs55706012	0.87[EUR][1000 genomes]
rs6903015	0.91[CEU][hapmap]
rs6923139	0.91[CEU][hapmap]
rs6939978	0.90[CEU][hapmap]
rs9379864	1.00[YRI][hapmap]
rs9467701	0.91[CEU][hapmap]
rs9467704	1.00[CEU][hapmap]
rs9467714	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	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
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
13	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
14	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
15	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
16	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
17	nsv518431	chr6:26148311-26211368	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
18	nsv526456	chr6:26148311-26211368	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
19	nsv883490	chr6:26172219-26231608	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	316 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs17598658	BTN3A2	cis	Whole Blood	GTEx
rs17598658	BTN3A2	cis	uninvolved skin	skin_eQTL
rs17598658	BTN3A2	cis	multi-tissue	Pritchard
rs17598658	BTN3A2	cis	Nerve Tibial	GTEx
rs17598658	BTN3A2	cis	Esophagus Muscularis	GTEx
rs17598658	BTN3A2	cis	Esophagus Mucosa	GTEx
rs17598658	BTN3A2	cis	Heart Left Ventricle	GTEx
rs17598658	BTN3A2	cis	lung	GTEx
rs17598658	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs17598658	BTN3A2	cis	Artery Aorta	GTEx
rs17598658	BTN3A2	cis	Thyroid	GTEx
rs17598658	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs17598658	BTN3A2	cis	Artery Tibial	GTEx
rs17598658	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs17598658	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs17598658	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs17598658	BTN3A2	cis	Muscle Skeletal	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26173000-26177800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26173200-26183400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:26173400-26179800	Weak transcription	Pancreas	Pancrea
4	chr6:26173800-26176000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:26173800-26176000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:26173800-26176000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:26173800-26176000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:26173800-26176000	Weak transcription	HMEC	breast
9	chr6:26173800-26176200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:26173800-26176200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:26173800-26176200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr6:26173800-26177800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:26173800-26183200	Weak transcription	NHEK	skin
14	chr6:26173800-26183400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:26173800-26183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:26173800-26183400	Weak transcription	HUVEC	blood vessel
17	chr6:26173800-26183800	Weak transcription	HSMMtube	muscle
18	chr6:26174200-26176000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:26174200-26176400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:26174200-26178400	Weak transcription	Colonic Mucosa	Colon
21	chr6:26174200-26182800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:26174200-26183400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:26174400-26180600	Weak transcription	Thymus	Thymus
24	chr6:26174800-26176000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr6:26174800-26176000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:26174800-26176000	Weak transcription	Hela-S3	cervix
27	chr6:26174800-26176200	Weak transcription	Fetal Thymus	thymus
28	chr6:26174800-26180600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:26174800-26183400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:26175200-26176200	Enhancers	Primary B cells from cord blood	blood
31	chr6:26175200-26183400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:26175400-26176200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:26175400-26176200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:26175600-26176000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:26175600-26176200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr6:26175600-26176200	Enhancers	Primary T cells from cord blood	blood
37	chr6:26175600-26176200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr6:26175600-26176200	Flanking Active TSS	Dnd41	blood
39	chr6:26175600-26176200	Flanking Active TSS	GM12878-XiMat	blood
40	chr6:26175800-26176000	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:26175800-26176000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:26175800-26176000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:26175800-26176000	Enhancers	A549	lung
44	chr6:26175800-26176000	Active TSS	K562	blood
45	chr6:26175800-26176200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr6:26175800-26176200	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:26175800-26176200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:26175800-26176200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr6:26175800-26176200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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