Variant report

Variant	rs2900463
Chromosome Location	chr9:100977457-100977458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100976860..100978461-chr9:101017333..101019221,2	MCF-7	breast:
2	chr9:100879928..100882828-chr9:100976182..100978819,2	MCF-7	breast:
3	chr9:100818654..100820478-chr9:100976673..100978536,2	MCF-7	breast:
4	chr9:100954026..100955906-chr9:100977446..100979664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095383	Chromatin interaction
ENSG00000106789	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10818669	0.86[AMR][1000 genomes]
rs10985366	0.81[AMR][1000 genomes]
rs10985441	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12343641	0.80[AMR][1000 genomes]
rs1435261	0.81[AMR][1000 genomes]
rs1469800	0.84[AMR][1000 genomes]
rs1469802	0.85[AMR][1000 genomes]
rs2023361	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181581	0.81[ASN][1000 genomes]
rs2417893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3739666	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739667	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780449	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780450	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780452	0.87[GIH][hapmap]
rs3780453	0.87[GIH][hapmap]
rs4743186	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743193	0.82[AMR][1000 genomes]
rs6478596	0.81[ASN][1000 genomes]
rs6478597	0.81[ASN][1000 genomes]
rs7021760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029585	0.87[GIH][hapmap]
rs733040	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7850360	0.86[AMR][1000 genomes]
rs7855855	0.95[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs942166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2900463	PRDM16	trans	multi-tissue	Pritchard
rs2900463	TBC1D2	cis	cerebellum	SCAN
rs2900463	HEMGN	cis	cerebellum	SCAN
rs2900463	CORO2A	cis	Lymphoblastoid	GTEx
rs2900463	CORO2A	cis	Whole Blood	GTEx
rs2900463	TBC1D2	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:100956000-100981000	Weak transcription	A549	lung
3	chr9:100958600-100985400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:100959600-100984400	Strong transcription	Osteobl	bone
5	chr9:100959800-100985200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
7	chr9:100965600-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:100968000-100987000	Weak transcription	Small Intestine	intestine
9	chr9:100968400-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:100968600-100985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:100968800-100984600	Weak transcription	K562	blood
15	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr9:100969000-100979000	Weak transcription	Fetal Brain Female	brain
18	chr9:100969000-100984800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:100969200-100985600	Strong transcription	Fetal Intestine Small	intestine
20	chr9:100969400-100980600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:100969400-100981000	Strong transcription	Placenta	Placenta
22	chr9:100969400-100981000	Weak transcription	Fetal Thymus	thymus
23	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
24	chr9:100969600-100997200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:100969800-100977800	Strong transcription	Primary T cells from cord blood	blood
26	chr9:100969800-100991800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:100970000-100985400	Strong transcription	Spleen	Spleen
28	chr9:100970200-101001600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:100970400-100983800	Strong transcription	HSMMtube	muscle
30	chr9:100971200-100977800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:100971200-100981000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:100971200-100981800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:100971200-100985200	Strong transcription	Lung	lung
34	chr9:100971400-100979600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr9:100971400-100982200	Weak transcription	Ovary	ovary
36	chr9:100971400-100985400	Strong transcription	Fetal Intestine Large	intestine
37	chr9:100971600-100979800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:100971600-100981000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:100971600-100982000	Weak transcription	Pancreas	Pancrea
40	chr9:100972400-100983800	Strong transcription	HSMM	muscle
41	chr9:100973000-100981800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:100973000-100985800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:100973200-100979200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:100973200-100981600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:100973400-100978200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:100973600-100980400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr9:100973800-100985400	Weak transcription	Stomach Mucosa	stomach
48	chr9:100974000-100978000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:100974000-100984800	Strong transcription	Esophagus	oesophagus
50	chr9:100974200-100979600	Strong transcription	Rectal Mucosa Donor 29	rectum

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