Variant report

Variant	rs303020
Chromosome Location	chr6:25137516-25137517
allele	C/G
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	STAT1	chr6:25136856-25137522	Hela-S3	cervix:	n/a	chr6:25137266-25137280 chr6:25137267-25137278
2	POLR2A	chr6:25136835-25139403	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:25137453-25139116	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:25136992-25139613	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA1	chr6:25136718-25138791	PBDE	blood:	n/a	chr6:25137782-25137792
6	POLR2A	chr6:25136994-25139133	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000219682	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs302974	1.00[CEU][hapmap]
rs303010	0.84[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap]
rs303011	0.84[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap]
rs303032	1.00[ASN][1000 genomes]
rs303033	1.00[ASN][1000 genomes]
rs45546139	0.82[EUR][1000 genomes]
rs59104926	0.82[EUR][1000 genomes]
rs6928303	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs73386254	1.00[ASN][1000 genomes]
rs73386288	1.00[ASN][1000 genomes]
rs7749575	1.00[ASN][1000 genomes]
rs7751844	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7759688	0.82[EUR][1000 genomes]
rs7760331	0.82[EUR][1000 genomes]
rs9461103	0.92[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap]
rs950877	1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303020	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
2	chr6:25124400-25138200	Weak transcription	Spleen	Spleen
3	chr6:25133800-25138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:25135200-25140200	Active TSS	Right Atrium	heart
5	chr6:25135400-25138200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:25136000-25137600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr6:25136000-25137800	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr6:25136000-25138800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:25136200-25139000	Active TSS	Left Ventricle	heart
11	chr6:25136200-25139600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:25136200-25140000	Active TSS	Aorta	Aorta
14	chr6:25136400-25137600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:25136400-25138200	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr6:25136400-25139200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr6:25136400-25139400	Active TSS	Brain Hippocampus Middle	brain
18	chr6:25136600-25137800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:25136600-25138000	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr6:25136600-25139400	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:25136600-25139600	Active TSS	Duodenum Mucosa	Duodenum
22	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:25136800-25137600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:25136800-25137600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:25136800-25137600	Enhancers	Fetal Heart	heart
26	chr6:25136800-25137800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:25136800-25137800	Enhancers	Hela-S3	cervix
28	chr6:25136800-25138000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:25136800-25138000	Genic enhancers	Placenta	Placenta
30	chr6:25136800-25138200	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr6:25136800-25138400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:25136800-25138400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr6:25136800-25138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:25136800-25138800	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr6:25136800-25139000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:25136800-25139000	Flanking Active TSS	Liver	Liver
37	chr6:25136800-25139000	Flanking Active TSS	Osteobl	bone
38	chr6:25136800-25139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr6:25136800-25139400	Active TSS	Brain Anterior Caudate	brain
40	chr6:25136800-25139400	Active TSS	Right Ventricle	heart
41	chr6:25136800-25140000	Active TSS	Ovary	ovary
42	chr6:25137000-25137600	Enhancers	Small Intestine	intestine
43	chr6:25137000-25137800	Enhancers	HUVEC	blood vessel
44	chr6:25137000-25138000	Weak transcription	Fetal Lung	lung
45	chr6:25137000-25138200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr6:25137000-25138200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:25137000-25138200	Enhancers	Fetal Muscle Leg	muscle
48	chr6:25137000-25138200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
49	chr6:25137000-25138400	Enhancers	Fetal Stomach	stomach
50	chr6:25137000-25139000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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