Variant report

Variant	rs4592653
Chromosome Location	chr16:70587124-70587125
allele	C/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	MAFK	chr16:70587017-70587318	Hela-S3	cervix:	n/a	chr16:70587161-70587181 chr16:70587159-70587173 chr16:70587164-70587178 chr16:70587163-70587179 chr16:70587160-70587175
2	POLR2A	chr16:70587037-70587408	K562	blood:	n/a	n/a
3	MAFK	chr16:70587026-70587351	K562	blood:	n/a	chr16:70587161-70587181 chr16:70587159-70587173 chr16:70587164-70587178 chr16:70587163-70587179 chr16:70587160-70587175
4	HEY1	chr16:70587016-70587326	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:70587003-70588024	U87	brain:	n/a	n/a
6	MAFK	chr16:70586972-70587923	IMR90	lung:	n/a	chr16:70587161-70587181 chr16:70587159-70587173 chr16:70587164-70587178 chr16:70587163-70587179 chr16:70587160-70587175
7	POLR2A	chr16:70587016-70587825	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:70587089-70587492	HL-60	blood:	n/a	n/a
9	MAFK	chr16:70587006-70587351	HepG2	liver:	n/a	chr16:70587161-70587181 chr16:70587159-70587173 chr16:70587164-70587178 chr16:70587163-70587179 chr16:70587160-70587175
10	MAZ	chr16:70587093-70588212	IMR90	lung:	n/a	chr16:70587776-70587786
11	MAFK	chr16:70586988-70587354	HepG2	liver:	n/a	chr16:70587161-70587181 chr16:70587159-70587173 chr16:70587164-70587178 chr16:70587163-70587179 chr16:70587160-70587175
12	POLR2A	chr16:70587084-70587438	K562	blood:	n/a	n/a
13	MAFF	chr16:70586996-70587359	HepG2	liver:	n/a	chr16:70587164-70587178 chr16:70587158-70587176
14	POLR2A	chr16:70587043-70587684	MCF-7	breast:	n/a	n/a
15	MAFF	chr16:70587003-70587339	K562	blood:	n/a	chr16:70587164-70587178 chr16:70587158-70587176
16	POLR2A	chr16:70586997-70588030	U87	brain:	n/a	n/a
17	POLR2A	chr16:70587118-70587420	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70583860..70585877-chr16:70586013..70587585,2	MCF-7	breast:
2	chr16:70581407..70583645-chr16:70584695..70587676,2	MCF-7	breast:
3	chr16:70585124..70587851-chr16:70588239..70589751,2	MCF-7	breast:
4	chr16:70586515..70589025-chr16:70601778..70603829,3	MCF-7	breast:
5	chr16:70584914..70587806-chr16:70588613..70590972,2	K562	blood:

Variant related genes	Relation type
SF3B3	TF binding region
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10852465	0.88[EUR][1000 genomes]
rs11075767	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11075768	0.97[EUR][1000 genomes]
rs11075769	0.91[EUR][1000 genomes]
rs11075770	0.96[CEU][hapmap];0.84[GIH][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs11075772	0.83[EUR][1000 genomes]
rs11640374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs11641683	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11643344	0.82[AFR][1000 genomes]
rs11643373	0.96[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11643823	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11645092	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11645214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11645287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs11645437	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11645585	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs11648402	0.96[CEU][hapmap];0.80[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs11649624	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11866400	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12446395	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs12597401	0.81[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12909	0.95[EUR][1000 genomes]
rs12925729	0.81[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12931402	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12933634	0.83[EUR][1000 genomes]
rs2168606	0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2288491	0.81[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2303793	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs33910368	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34567847	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34890962	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3762171	0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4277334	0.80[EUR][1000 genomes]
rs4284632	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs4324119	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4436771	0.96[CEU][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4513092	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs58963621	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6499320	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs6499321	0.97[EUR][1000 genomes]
rs71401814	0.95[EUR][1000 genomes]
rs7192865	0.84[JPT][hapmap];0.91[LWK][hapmap];0.83[YRI][hapmap]
rs7194521	0.81[EUR][1000 genomes]
rs7195030	0.91[EUR][1000 genomes]
rs7197262	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7197840	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7198317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7199859	0.84[EUR][1000 genomes]
rs7200430	0.96[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7201750	0.96[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs7204583	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs722579	0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs8045651	0.84[EUR][1000 genomes]
rs8046881	0.93[EUR][1000 genomes]
rs8047409	0.80[EUR][1000 genomes]
rs8049277	0.81[EUR][1000 genomes]
rs8049641	0.96[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs8049786	0.91[EUR][1000 genomes]
rs8051506	0.81[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs8052031	0.85[EUR][1000 genomes]
rs8052125	0.96[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs8053436	0.81[AFR][1000 genomes]
rs8057610	0.96[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs8062178	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs8063990	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs8064013	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9635522	0.97[EUR][1000 genomes]
rs9929904	0.83[EUR][1000 genomes]
rs9936225	0.96[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4592653	RP11-296I10.6	cis	Thyroid	GTEx
rs4592653	COG4	cis	Whole Blood	GTEx
rs4592653	EXOSC6	cis	parietal	SCAN
rs4592653	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs4592653	SF3B3	cis	cerebellum	SCAN
rs4592653	PDPR	cis	parietal	SCAN
rs4592653	WWP2	cis	cerebellum	SCAN
rs4592653	SF3B3	cis	parietal	SCAN
rs4592653	RP11-296I10.6	cis	Artery Tibial	GTEx
rs4592653	EXOSC6	cis	cerebellum	SCAN
rs4592653	IL34	cis	parietal	SCAN
rs4592653	TMCO7	cis	parietal	SCAN
rs4592653	PDPR	cis	cerebellum	SCAN
rs4592653	C16orf86	cis	cerebellum	SCAN
rs4592653	WWP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70559400-70606200	Strong transcription	Fetal Stomach	stomach
2	chr16:70560400-70605200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr16:70560400-70605600	Strong transcription	Placenta	Placenta
4	chr16:70560400-70607800	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr16:70560600-70598800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr16:70560600-70609600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:70560800-70608800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:70561000-70605200	Strong transcription	Fetal Muscle Leg	muscle
9	chr16:70561000-70608800	Strong transcription	Fetal Thymus	thymus
10	chr16:70561000-70609000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr16:70561000-70609400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr16:70561000-70610000	Strong transcription	Thymus	Thymus
13	chr16:70561200-70587200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr16:70561200-70602000	Strong transcription	Fetal Intestine Large	intestine
15	chr16:70561200-70609400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr16:70561200-70609600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr16:70561400-70587200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:70561400-70605200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:70561400-70607600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr16:70561400-70609000	Strong transcription	Primary B cells from cord blood	blood
21	chr16:70561400-70610000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:70561600-70609000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr16:70561600-70609200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr16:70561600-70609600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr16:70561600-70609800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr16:70562200-70609600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr16:70562600-70594400	Strong transcription	Lung	lung
28	chr16:70562800-70608800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr16:70562800-70609000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr16:70563000-70590000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:70563000-70606400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:70563200-70602200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:70563200-70605200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:70563200-70605800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr16:70563200-70606600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:70563200-70609000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr16:70563200-70609600	Strong transcription	Primary T cells from cord blood	blood
38	chr16:70563200-70609800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr16:70563200-70610000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr16:70563400-70608400	Strong transcription	Fetal Brain Female	brain
41	chr16:70563400-70609000	Strong transcription	Brain Anterior Caudate	brain
42	chr16:70563400-70609800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:70563400-70610000	Strong transcription	A549	lung
44	chr16:70563600-70607400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr16:70563600-70608200	Strong transcription	HepG2	liver
46	chr16:70563600-70609600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr16:70563800-70593400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr16:70563800-70595600	Strong transcription	Liver	Liver
49	chr16:70563800-70606200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr16:70563800-70608600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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