Variant report

Variant	rs4939146
Chromosome Location	chr11:57272612-57272613
allele	A/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	CEBPB	chr11:57272476-57272630	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SLC43A1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10160419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10792101	0.88[JPT][hapmap]
rs11229042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11229044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12275916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12296041	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4938869	0.88[JPT][hapmap]
rs4939147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59972624	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61886990	0.82[EUR][1000 genomes]
rs61886993	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6591429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7933797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7934626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4939146	OR9G1	cis	cerebellum	SCAN
rs4939146	CD5	cis	parietal	SCAN
rs4939146	OR5M8	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:57253800-57276400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:57253800-57279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:57256400-57273000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:57257400-57281400	Weak transcription	Primary T cells from cord blood	blood
8	chr11:57258800-57279200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
11	chr11:57261400-57281400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:57261800-57279600	Weak transcription	Dnd41	blood
13	chr11:57267200-57279400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr11:57267600-57274600	Genic enhancers	HepG2	liver
15	chr11:57267600-57280200	Weak transcription	Primary B cells from cord blood	blood
16	chr11:57267600-57281200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:57267600-57281600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:57267800-57273600	Weak transcription	Osteobl	bone
19	chr11:57267800-57274000	Weak transcription	HSMM	muscle
20	chr11:57267800-57280600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:57267800-57281400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:57267800-57281400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:57267800-57281400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr11:57267800-57281600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:57267800-57281600	Weak transcription	NH-A	brain
26	chr11:57267800-57281800	Weak transcription	Aorta	Aorta
27	chr11:57268000-57276400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:57268000-57276600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:57268000-57279600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:57268000-57281000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:57268000-57281800	Weak transcription	Small Intestine	intestine
32	chr11:57268200-57280000	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:57268200-57280400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:57268200-57280800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:57268200-57281600	Weak transcription	Brain Angular Gyrus	brain
36	chr11:57268400-57281800	Weak transcription	Fetal Lung	lung
37	chr11:57268600-57280400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:57268600-57280800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:57268600-57280800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:57268600-57281800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:57268800-57280200	Weak transcription	NHLF	lung
42	chr11:57268800-57281200	Weak transcription	Lung	lung
43	chr11:57268800-57281600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:57269000-57273400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr11:57269000-57279200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:57269000-57280200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:57269000-57281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:57269000-57281400	Weak transcription	Left Ventricle	heart
49	chr11:57269800-57280600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:57269800-57281200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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