Variant report

Variant	rs17405811
Chromosome Location	chr4:15685805-15685806
allele	G/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	POLR2A	chr4:15682912-15686646	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:15681678..15685124-chr4:15685309..15687808,5	MCF-7	breast:
2	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
3	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:
4	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:

Variant related genes	Relation type
FAM200B	TF binding region
FBXL5	TF binding region
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10005305	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008878	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10015827	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10017222	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10025875	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10433813	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722300	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722854	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap]
rs11729955	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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730088	0.81[CEU][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732953	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11735063	1.00[CHB][hapmap]
rs11947383	0.96[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13134177	0.87[ASN][1000 genomes]
rs17476642	1.00[CHB][hapmap]
rs1786	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs28394730	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28604503	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35519415	0.83[EUR][1000 genomes]
rs3756246	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs3756247	1.00[CHB][hapmap]
rs3775956	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4301111	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs4396986	1.00[CHB][hapmap]
rs4423870	1.00[CHB][hapmap]
rs4549375	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs4554069	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414764	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs6449152	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6815254	1.00[CHB][hapmap]
rs6815296	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];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824422	1.00[CHB][hapmap]
rs6826058	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs6827406	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6839654	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs6848779	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434484	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9994518	0.88[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17405811	FAM200B	cis	cerebellum	SCAN
rs17405811	FAM200B	cis	parietal	SCAN
rs17405811	FGFBP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15681800-15686200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr4:15683600-15687600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr4:15683800-15686800	Weak transcription	Gastric	stomach
4	chr4:15684000-15686200	Weak transcription	Esophagus	oesophagus
5	chr4:15684000-15686200	Weak transcription	Spleen	Spleen
6	chr4:15684000-15688000	Weak transcription	Pancreas	Pancrea
7	chr4:15684000-15691000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:15684000-15692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:15684000-15697000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:15684000-15704400	Weak transcription	Left Ventricle	heart
11	chr4:15684200-15687400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:15684400-15686200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:15684400-15686200	Weak transcription	Placenta	Placenta
14	chr4:15684400-15687200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr4:15684400-15692200	Weak transcription	Right Ventricle	heart
16	chr4:15684600-15686000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:15684600-15686000	Enhancers	Fetal Heart	heart
18	chr4:15684600-15686200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:15684600-15686200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:15684600-15686200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr4:15684600-15686200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:15684600-15686400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:15684600-15686600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:15684600-15686600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:15684600-15686800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:15684600-15686800	Enhancers	Brain Substantia Nigra	brain
27	chr4:15684600-15687000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr4:15684600-15687000	Weak transcription	Ovary	ovary
29	chr4:15684600-15687200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:15684600-15687200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr4:15684600-15690800	Weak transcription	HSMMtube	muscle
32	chr4:15684800-15686000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:15684800-15686000	Enhancers	Brain Hippocampus Middle	brain
34	chr4:15684800-15686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:15684800-15686200	Enhancers	Colon Smooth Muscle	Colon
36	chr4:15684800-15686400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr4:15684800-15686400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr4:15684800-15686400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr4:15684800-15686400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:15684800-15686600	Enhancers	Fetal Kidney	kidney
41	chr4:15684800-15686800	Weak transcription	Fetal Stomach	stomach
42	chr4:15684800-15687000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr4:15684800-15687000	Enhancers	Brain Anterior Caudate	brain
44	chr4:15684800-15687000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:15684800-15687200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:15684800-15687200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:15684800-15687800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:15684800-15688000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr4:15684800-15688000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:15684800-15690800	Enhancers	Primary neutrophils fromperipheralblood	blood

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