Variant report

Variant	rs1401417
Chromosome Location	chr11:45880110-45880111
allele	C/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	POLR2A	chr11:45878353-45880252	HepG2	liver:	n/a	n/a
2	ZNF263	chr11:45880018-45880667	HEK293-T-REx	kidney:	n/a	chr11:45880234-45880243 chr11:45880220-45880241
3	MXI1	chr11:45880061-45882054	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:45879797..45882942-chr11:45890045..45892313,4	K562	blood:
2	chr11:45867823..45873583-chr11:45876186..45881298,10	MCF-7	breast:
3	chr11:45879680..45881437-chr11:45942342..45944046,2	MCF-7	breast:

Variant related genes	Relation type
CRY2	TF binding region
ENSG00000121671	Chromatin interaction
ENSG00000165905	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10462026	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838526	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038668	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs11038670	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11038671	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11038675	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs11038679	0.98[EUR][1000 genomes]
rs11038680	0.98[EUR][1000 genomes]
rs11038683	0.98[EUR][1000 genomes]
rs11038685	0.98[EUR][1000 genomes]
rs11038686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11038689	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038699	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11038700	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038703	0.83[EUR][1000 genomes]
rs12364060	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787106	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787136	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756030	0.95[EUR][1000 genomes]
rs4756032	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923741	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56330140	0.98[EUR][1000 genomes]
rs7121775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7123390	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72900638	0.92[EUR][1000 genomes]
rs72900650	0.92[EUR][1000 genomes]
rs72900652	0.92[EUR][1000 genomes]
rs72900692	0.98[EUR][1000 genomes]
rs72900694	0.98[EUR][1000 genomes]
rs72902412	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902439	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877412	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1401417	MAPK8IP1	cis	Whole Blood	GTEx
rs1401417	MAPK8IP1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45869800-45883600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45870800-45880800	Weak transcription	HMEC	breast
3	chr11:45872600-45880200	Weak transcription	Aorta	Aorta
4	chr11:45874200-45904200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr11:45875200-45882600	Genic enhancers	Liver	Liver
6	chr11:45875200-45905600	Strong transcription	Primary T cells from cord blood	blood
7	chr11:45875400-45893400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:45875800-45904200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:45876400-45904200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:45876600-45882600	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr11:45876600-45882600	Enhancers	Right Atrium	heart
12	chr11:45876800-45881800	Enhancers	Right Ventricle	heart
13	chr11:45876800-45882600	Genic enhancers	Fetal Muscle Leg	muscle
14	chr11:45876800-45882600	Genic enhancers	Fetal Stomach	stomach
15	chr11:45876800-45894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:45876800-45895600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:45876800-45895600	Strong transcription	Thymus	Thymus
18	chr11:45876800-45900200	Strong transcription	Primary B cells from cord blood	blood
19	chr11:45876800-45903600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:45876800-45904600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:45877000-45881000	Genic enhancers	Brain Hippocampus Middle	brain
22	chr11:45877000-45885800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:45877000-45885800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:45877000-45885800	Strong transcription	Dnd41	blood
25	chr11:45877000-45885800	Strong transcription	GM12878-XiMat	blood
26	chr11:45877000-45885800	Strong transcription	K562	blood
27	chr11:45877000-45886000	Strong transcription	HepG2	liver
28	chr11:45877000-45893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:45877000-45895600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:45877200-45880600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:45877200-45881200	Genic enhancers	NHLF	lung
32	chr11:45877200-45881800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr11:45877200-45882600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:45877200-45883800	Genic enhancers	Left Ventricle	heart
35	chr11:45877200-45886000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:45877200-45893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:45877400-45880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:45877400-45880800	Strong transcription	Hela-S3	cervix
39	chr11:45877400-45882600	Genic enhancers	Lung	lung
40	chr11:45877400-45887200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr11:45877400-45899800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:45877400-45900200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:45877400-45903800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:45877400-45904200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:45877600-45880200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:45877600-45880400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:45877600-45880400	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr11:45877600-45881000	Genic enhancers	Brain Angular Gyrus	brain
49	chr11:45877600-45882400	Genic enhancers	Osteobl	bone
50	chr11:45877600-45882800	Genic enhancers	Brain Cingulate Gyrus	brain

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