Variant report

Variant	rs17427842
Chromosome Location	chr15:76220161-76220162
allele	C/T
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	STAT3	chr15:76220130-76220263	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr15:76220039-76220244	MCF10A-Er-Src	breast:	n/a	chr15:76220097-76220111 chr15:76220098-76220109 chr15:76220100-76220108
3	RUNX3	chr15:76219969-76220470	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76218432..76221221-chr15:76222501..76224322,2	K562	blood:

Variant related genes	Relation type
FBXO22	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11636891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638364	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12898403	0.85[EUR][1000 genomes]
rs12899204	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909182	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12910038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910494	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12911337	0.82[ASW][hapmap]
rs12913434	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915152	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1499063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17427165	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17427298	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2441930	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs335685	0.81[JPT][hapmap]
rs35031760	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35656041	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3764189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62027608	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62027611	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62028932	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028936	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72734564	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8182037	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1044733	chr15:76120924-76228880	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv984193	chr15:76214943-76221739	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17427842	FBXO22	cis	parietal	SCAN
rs17427842	ODF3L1	cis	parietal	SCAN
rs17427842	NRG4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76198000-76231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:76198200-76232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:76198400-76225000	Weak transcription	Fetal Kidney	kidney
4	chr15:76198600-76226400	Weak transcription	Fetal Brain Male	brain
5	chr15:76203800-76230200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:76207000-76226600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:76207000-76228200	Weak transcription	Brain Substantia Nigra	brain
8	chr15:76207000-76228200	Weak transcription	Colonic Mucosa	Colon
9	chr15:76207000-76232000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:76207200-76225000	Weak transcription	Spleen	Spleen
11	chr15:76207200-76226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:76207400-76222200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:76207400-76222200	Weak transcription	Brain Angular Gyrus	brain
14	chr15:76207400-76223000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:76208000-76222400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:76208400-76232800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:76209000-76225000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:76209000-76225000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:76209800-76222800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:76210200-76222200	Strong transcription	Primary T cells from cord blood	blood
21	chr15:76210800-76225000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:76211400-76240200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:76212200-76222600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:76212400-76223400	Strong transcription	HepG2	liver
25	chr15:76213000-76221800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:76213000-76222200	Weak transcription	Brain Anterior Caudate	brain
27	chr15:76213000-76224200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:76214000-76222400	Weak transcription	Placenta	Placenta
29	chr15:76214600-76220200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:76214800-76222800	Weak transcription	Fetal Thymus	thymus
31	chr15:76215000-76220400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:76215000-76226600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:76215200-76222200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:76215200-76222200	Weak transcription	Osteobl	bone
35	chr15:76215200-76222800	Weak transcription	NH-A	brain
36	chr15:76215200-76223200	Weak transcription	Ovary	ovary
37	chr15:76215200-76225000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:76215200-76225000	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:76215200-76225000	Weak transcription	Fetal Lung	lung
40	chr15:76215200-76225000	Weak transcription	NHDF-Ad	bronchial
41	chr15:76215200-76229200	Weak transcription	Esophagus	oesophagus
42	chr15:76215400-76221000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:76215400-76222200	Weak transcription	Adipose Nuclei	Adipose
44	chr15:76215400-76222200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:76215400-76222200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:76215400-76227000	Weak transcription	Small Intestine	intestine
47	chr15:76215600-76221200	Weak transcription	HUVEC	blood vessel
48	chr15:76215600-76224200	Weak transcription	Fetal Intestine Small	intestine
49	chr15:76215800-76222200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:76216200-76220200	Strong transcription	Muscle Satellite Cultured Cells	--

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