Variant report

Variant	rs277655
Chromosome Location	chr3:100044587-100044588
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100041336..100046382-chr3:100052282..100055066,6	MCF-7	breast:
2	chr3:100036672..100038736-chr3:100043578..100046026,2	K562	blood:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1036770	0.83[ASN][1000 genomes]
rs10936157	0.95[CHB][hapmap]
rs1214371	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1609481	1.00[CHB][hapmap]
rs2028494	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs2029162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2316246	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs277637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277656	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs277660	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34547730	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35805111	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35939236	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36013739	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3772698	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs384528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3862050	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345098	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4552390	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs4928118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4928119	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs4928169	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs6804963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs967608	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9863237	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9968163	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs277655	TAP1	trans	brain	seeQTL
rs277655	CCR1	trans	brain	seeQTL
rs277655	CXCL10	trans	brain	seeQTL
rs277655	LY96	trans	brain	seeQTL
rs277655	RGS16	trans	brain	seeQTL
rs277655	TYMP	trans	brain	seeQTL
rs277655	IRF1	trans	brain	seeQTL
rs277655	STAT1	trans	brain	seeQTL
rs277655	IFI30	trans	brain	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100053200	Weak transcription	Gastric	stomach
2	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
4	chr3:100007000-100045000	Weak transcription	Lung	lung
5	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
6	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:100019600-100053000	Weak transcription	Colonic Mucosa	Colon
9	chr3:100020600-100053000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:100020600-100053000	Weak transcription	Hela-S3	cervix
11	chr3:100021800-100052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:100021800-100053000	Weak transcription	Psoas Muscle	Psoas
13	chr3:100022000-100047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:100022000-100052800	Weak transcription	Pancreas	Pancrea
15	chr3:100025800-100053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:100025800-100053000	Weak transcription	Right Ventricle	heart
17	chr3:100026000-100052600	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:100026000-100052800	Weak transcription	Thymus	Thymus
19	chr3:100026400-100045600	Weak transcription	HSMMtube	muscle
20	chr3:100026400-100052800	Weak transcription	NHEK	skin
21	chr3:100026400-100053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:100026600-100048600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:100026600-100052800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:100029600-100053000	Weak transcription	Brain Substantia Nigra	brain
25	chr3:100030200-100049800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:100030200-100053000	Weak transcription	Fetal Brain Female	brain
27	chr3:100031000-100053000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:100031200-100051200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:100033200-100046600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:100033600-100044600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:100033600-100045000	Weak transcription	Fetal Stomach	stomach
32	chr3:100033600-100052800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:100034800-100046600	Strong transcription	HSMM	muscle
34	chr3:100035000-100053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:100035600-100053000	Weak transcription	Stomach Mucosa	stomach
36	chr3:100036000-100052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:100036000-100053000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:100036200-100046600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:100036200-100047400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:100036200-100052800	Weak transcription	A549	lung
41	chr3:100036200-100053000	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:100036400-100046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:100036600-100046600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:100037000-100053000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:100037400-100053000	Weak transcription	GM12878-XiMat	blood
46	chr3:100038400-100045000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:100038800-100053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:100039000-100053000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:100039000-100053000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:100039200-100053000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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