Variant report

Variant	rs9104
Chromosome Location	chr6:26378149-26378150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26370389..26374393-chr6:26375542..26380304,5	K562	blood:
2	chr6:26376258..26380187-chr6:26381333..26383262,3	K562	blood:
3	chr6:26373307..26375855-chr6:26376435..26379484,4	K562	blood:

Variant related genes	Relation type
ENSG00000186470	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10807008	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs10946824	1.00[CHD][hapmap]
rs10946826	1.00[CHD][hapmap]
rs10946829	1.00[CHD][hapmap]
rs1131936	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12191917	1.00[CHD][hapmap]
rs12201546	1.00[CHD][hapmap]
rs12203176	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs12206621	1.00[CEU][hapmap]
rs12206812	1.00[CHD][hapmap]
rs12207930	1.00[CHD][hapmap]
rs12208788	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12214444	1.00[CHD][hapmap]
rs12214924	1.00[CHD][hapmap]
rs12664899	0.85[CEU][hapmap]
rs13437351	1.00[JPT][hapmap]
rs14232	0.98[EUR][1000 genomes]
rs16891666	1.00[JPT][hapmap]
rs17537465	0.85[CEU][hapmap]
rs17539219	1.00[CHD][hapmap]
rs17610161	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs2281027	1.00[JPT][hapmap]
rs2393652	1.00[CHD][hapmap]
rs2893845	1.00[CHD][hapmap]
rs2893847	1.00[CHD][hapmap]
rs2893848	1.00[CHD][hapmap]
rs35183513	0.82[EUR][1000 genomes]
rs3734541	1.00[JPT][hapmap]
rs3757141	1.00[JPT][hapmap]
rs3757147	1.00[JPT][hapmap]
rs3846841	1.00[JPT][hapmap]
rs3846842	1.00[JPT][hapmap]
rs3846843	1.00[CHD][hapmap]
rs3846848	1.00[CHD][hapmap]
rs3857549	1.00[JPT][hapmap]
rs3902051	0.85[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap]
rs4476815	1.00[JPT][hapmap]
rs4609015	1.00[CHD][hapmap]
rs4711108	0.84[CEU][hapmap]
rs4712982	0.82[EUR][1000 genomes]
rs4712986	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4712988	0.85[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap]
rs4712990	1.00[CHD][hapmap]
rs4712993	1.00[CHD][hapmap]
rs4712994	1.00[CHD][hapmap]
rs4712996	1.00[CHD][hapmap]
rs55827419	0.80[EUR][1000 genomes]
rs55984635	0.80[EUR][1000 genomes]
rs6456715	0.82[EUR][1000 genomes]
rs6456716	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs6456718	0.80[EUR][1000 genomes]
rs6456720	1.00[JPT][hapmap]
rs6456725	1.00[JPT][hapmap]
rs6456726	1.00[JPT][hapmap]
rs6900725	1.00[CHD][hapmap]
rs6901118	1.00[JPT][hapmap]
rs6907857	1.00[JPT][hapmap]
rs6910921	1.00[JPT][hapmap]
rs6910993	1.00[JPT][hapmap]
rs6911470	1.00[JPT][hapmap]
rs6920986	1.00[CHD][hapmap]
rs6926878	1.00[CHD][hapmap]
rs6929846	1.00[JPT][hapmap]
rs72836457	0.80[EUR][1000 genomes]
rs72836479	0.81[EUR][1000 genomes]
rs72841510	0.82[EUR][1000 genomes]
rs72841540	0.82[EUR][1000 genomes]
rs7355	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7356849	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7356982	1.00[JPT][hapmap]
rs7744254	1.00[CHD][hapmap]
rs7751280	1.00[CHD][hapmap]
rs7751645	1.00[JPT][hapmap]
rs7768108	1.00[CHD][hapmap]
rs7769926	1.00[JPT][hapmap]
rs7770214	1.00[CHD][hapmap]
rs7773913	1.00[JPT][hapmap]
rs9295692	1.00[JPT][hapmap]
rs9461245	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs9461252	1.00[JPT][hapmap]
rs9461253	1.00[JPT][hapmap]
rs9461254	1.00[JPT][hapmap]
rs9467716	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9467717	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9467718	0.80[EUR][1000 genomes]
rs9467721	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9467748	1.00[JPT][hapmap]
rs9467753	1.00[JPT][hapmap]
rs9467757	1.00[JPT][hapmap]
rs9467759	1.00[JPT][hapmap]
rs9467760	0.85[JPT][hapmap]
rs9467761	1.00[JPT][hapmap]
rs9467768	1.00[JPT][hapmap]
rs9467771	1.00[JPT][hapmap]
rs9467788	1.00[JPT][hapmap]
rs9688949	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]

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	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	nsv527328	chr6:26372786-26379537	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv970086	chr6:26374877-26378621	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9104	BTN3A2	cis	parietal	SCAN
rs9104	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs9104	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9104	BTN3A2	cis	multi-tissue	Pritchard
rs9104	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs9104	BTN3A1	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26366000-26382600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:26366000-26383000	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:26366000-26383200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:26366000-26383200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:26366000-26383200	Weak transcription	Pancreas	Pancrea
6	chr6:26366000-26383200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:26366000-26383200	Weak transcription	HSMMtube	muscle
8	chr6:26366000-26383400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:26366200-26382400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:26366200-26383200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:26366200-26383200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:26367000-26383000	Weak transcription	NHEK	skin
13	chr6:26367000-26383200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:26367800-26378600	Weak transcription	Small Intestine	intestine
15	chr6:26369400-26378200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:26369800-26378200	Strong transcription	Thymus	Thymus
17	chr6:26369800-26383000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:26370400-26378200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:26370400-26383000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:26370800-26379000	Strong transcription	Primary T cells from cord blood	blood
21	chr6:26370800-26383200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:26371000-26383200	Weak transcription	Right Ventricle	heart
23	chr6:26372000-26378200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:26372600-26378200	Strong transcription	Lung	lung
25	chr6:26373400-26378200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:26374000-26382400	Weak transcription	Dnd41	blood
27	chr6:26374600-26378200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:26375200-26383200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:26375200-26383200	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:26375200-26383200	Weak transcription	Fetal Lung	lung
31	chr6:26375200-26383200	Weak transcription	Osteobl	bone
32	chr6:26375400-26383000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:26375600-26383200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:26375600-26383200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:26375800-26378400	Strong transcription	Fetal Thymus	thymus
36	chr6:26375800-26381400	Weak transcription	HepG2	liver
37	chr6:26375800-26382800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:26375800-26383000	Weak transcription	Brain Anterior Caudate	brain
39	chr6:26375800-26383000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:26375800-26383000	Weak transcription	Stomach Mucosa	stomach
41	chr6:26375800-26383200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:26375800-26383200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:26375800-26383200	Weak transcription	Placenta	Placenta
44	chr6:26375800-26383200	Weak transcription	Hela-S3	cervix
45	chr6:26376000-26378200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:26376000-26381200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:26376000-26383000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:26376000-26383200	Weak transcription	Esophagus	oesophagus
49	chr6:26376000-26383200	Weak transcription	Ovary	ovary
50	chr6:26376000-26383400	Weak transcription	Gastric	stomach

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