Variant report

Variant	rs4392990
Chromosome Location	chr9:19051028-19051029
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19050026..19052622-chr9:19058219..19060617,2	K562	blood:
2	chr9:19048960..19051096-chr9:19378749..19380850,2	MCF-7	breast:
3	chr9:19051025..19055237-chr9:19064013..19066512,4	MCF-7	breast:
4	chr9:19049276..19051385-chr9:19371232..19373694,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272842	Chromatin interaction
ENSG00000147874	Chromatin interaction
ENSG00000137154	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10122990	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10123400	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10123520	0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10123624	0.89[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs10125646	0.83[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125677	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1048169	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757024	0.84[CEU][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10757025	0.85[ASN][1000 genomes]
rs10811103	0.81[ASN][1000 genomes]
rs10811104	0.85[ASN][1000 genomes]
rs10811107	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10811108	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811110	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs10963921	0.84[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs10963924	0.84[CEU][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs10963925	0.86[CEU][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10963942	0.94[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11515236	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs1154672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12236347	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs12343169	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12380322	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13287117	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13287517	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1932457	0.89[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2130570	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2130571	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2233798	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35133951	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4394488	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4439216	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4977278	0.85[ASN][1000 genomes]
rs4977490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs4977492	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62563593	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62563594	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6475311	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6475312	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475313	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6475314	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6475315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs68092871	0.84[ASN][1000 genomes]
rs7022450	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7022576	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs7022807	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7026281	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7027346	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7035738	0.83[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs7036118	0.84[CEU][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs7036182	0.83[CEU][hapmap];0.84[ASN][1000 genomes]
rs7036301	0.84[CEU][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs7037772	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7037787	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043115	0.85[ASN][1000 genomes]
rs7043507	0.85[ASN][1000 genomes]
rs7045844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7467137	0.84[JPT][hapmap]
rs7467618	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7850487	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7854858	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs7854974	0.85[ASN][1000 genomes]
rs7855250	0.84[ASN][1000 genomes]
rs7856768	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7859259	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs9298795	0.86[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	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4392990	RRAGA	cis	cerebellum	SCAN
rs4392990	IFNA16	cis	cerebellum	SCAN
rs4392990	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048400-19051200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:19048400-19051200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr9:19048400-19051200	Active TSS	Colonic Mucosa	Colon
4	chr9:19048400-19051200	Active TSS	Right Ventricle	heart
5	chr9:19048400-19051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr9:19048400-19051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr9:19048400-19051600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:19048400-19051800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:19048400-19051800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr9:19048600-19051200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:19048600-19051200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:19048600-19051200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:19048600-19051200	Active TSS	Psoas Muscle	Psoas
14	chr9:19048600-19051200	Active TSS	Right Atrium	heart
15	chr9:19048600-19051200	Active TSS	GM12878-XiMat	blood
16	chr9:19048600-19051400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:19048800-19051200	Active TSS	Left Ventricle	heart
18	chr9:19048800-19051200	Active TSS	Ovary	ovary
19	chr9:19048800-19051800	Active TSS	HMEC	breast
20	chr9:19048800-19052000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:19048800-19052000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:19049000-19051200	Active TSS	NHLF	lung
23	chr9:19049000-19051400	Active TSS	Pancreas	Pancrea
24	chr9:19049000-19052000	Active TSS	Osteobl	bone
25	chr9:19049200-19051200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:19049400-19051200	Active TSS	Fetal Muscle Trunk	muscle
27	chr9:19049600-19051200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr9:19049600-19051200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:19049600-19051400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:19049800-19051200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr9:19049800-19051400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr9:19049800-19051400	Flanking Active TSS	HUVEC	blood vessel
33	chr9:19049800-19052000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr9:19050000-19051200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr9:19050000-19051200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr9:19050000-19051400	Flanking Active TSS	Liver	Liver
37	chr9:19050000-19052000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr9:19050000-19052000	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr9:19050200-19051200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:19050200-19051400	Flanking Active TSS	Hela-S3	cervix
41	chr9:19050200-19051600	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr9:19050200-19051800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr9:19050200-19051800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
44	chr9:19050200-19052000	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr9:19050200-19052000	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr9:19050400-19051200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr9:19050400-19051400	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr9:19050400-19051600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:19050400-19051600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:19050400-19051600	Flanking Active TSS	Fetal Brain Male	brain

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