Variant report

Variant	rs2873297
Chromosome Location	chr11:8791227-8791228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8713389..8715952-chr11:8790656..8792768,2	K562	blood:
2	chr11:8708263..8710064-chr11:8790794..8793308,2	MCF-7	breast:
3	chr11:8704319..8705885-chr11:8789262..8791873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254665	Chromatin interaction
ENSG00000200983	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10160684	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10500705	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10500707	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs10732515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10734636	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10734637	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743087	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743089	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769952	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769953	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769954	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1079452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042058	0.95[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11042066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042068	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11042077	0.83[MEX][hapmap]
rs11603335	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12420964	0.88[LWK][hapmap];0.87[YRI][hapmap]
rs2173999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292045	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2292046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34090393	0.83[EUR][1000 genomes]
rs34524863	0.87[EUR][1000 genomes]
rs35670750	0.87[EUR][1000 genomes]
rs3763920	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812762	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs3842991	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3844099	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850933	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3862352	0.82[EUR][1000 genomes]
rs3913547	0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4929910	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929931	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4929934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929936	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6484008	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6484425	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7120004	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7934519	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7952335	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs905289	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2873297	SNORA45	cis	cerebellum	SCAN
rs2873297	OR51F1	cis	parietal	SCAN
rs2873297	RPL27A	cis	cerebellum	SCAN
rs2873297	MRPL17	cis	cerebellum	SCAN
rs2873297	RPL27A	cis	parietal	SCAN
rs2873297	TMEM9B	cis	parietal	SCAN
rs2873297	HBB	cis	cerebellum	SCAN
rs2873297	STK33	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8777400-8795800	Enhancers	Rectal Smooth Muscle	rectum
2	chr11:8779600-8799600	Weak transcription	Fetal Brain Male	brain
3	chr11:8780000-8792400	Weak transcription	HepG2	liver
4	chr11:8781400-8794600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:8782000-8791600	Enhancers	Colon Smooth Muscle	Colon
6	chr11:8784000-8794200	Weak transcription	Colonic Mucosa	Colon
7	chr11:8785000-8791400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr11:8785200-8799400	Enhancers	Fetal Heart	heart
9	chr11:8786400-8794200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:8786600-8791400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:8786600-8791400	Enhancers	Right Ventricle	heart
12	chr11:8786600-8791600	Enhancers	Left Ventricle	heart
13	chr11:8786600-8791800	Enhancers	NHDF-Ad	bronchial
14	chr11:8786600-8791800	Enhancers	NHLF	lung
15	chr11:8786600-8795400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:8786600-8795400	Enhancers	Stomach Mucosa	stomach
17	chr11:8786600-8798000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:8786600-8803000	Enhancers	Ovary	ovary
19	chr11:8786800-8792400	Enhancers	HSMM	muscle
20	chr11:8787000-8791400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr11:8787000-8791800	Enhancers	Fetal Muscle Leg	muscle
22	chr11:8787000-8797800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr11:8787600-8791400	Enhancers	NHEK	skin
24	chr11:8787600-8795000	Weak transcription	Fetal Intestine Large	intestine
25	chr11:8787800-8791400	Enhancers	Esophagus	oesophagus
26	chr11:8788000-8791400	Enhancers	Psoas Muscle	Psoas
27	chr11:8788000-8791400	Enhancers	Right Atrium	heart
28	chr11:8788200-8791400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:8788200-8792400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:8788200-8794200	Weak transcription	Gastric	stomach
31	chr11:8788200-8797000	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:8788600-8792600	Weak transcription	Aorta	Aorta
33	chr11:8788600-8799600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:8788800-8792800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:8788800-8794200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr11:8788800-8794200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:8788800-8794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:8788800-8801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:8788800-8808400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:8789000-8791400	Enhancers	Osteobl	bone
41	chr11:8789000-8795400	Enhancers	HMEC	breast
42	chr11:8789000-8801200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:8789400-8791400	Enhancers	K562	blood
44	chr11:8789400-8794800	Weak transcription	Brain Anterior Caudate	brain
45	chr11:8789400-8797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:8789400-8797400	Weak transcription	Brain Substantia Nigra	brain
47	chr11:8789400-8807600	Weak transcription	Fetal Kidney	kidney
48	chr11:8789600-8799400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:8789600-8805800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:8789800-8791400	Enhancers	Hela-S3	cervix

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