Variant report

Variant	rs7190039
Chromosome Location	chr16:70606517-70606518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:70606329-70607020	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:70605969-70608018	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:70606056-70606575	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:70606482-70606977	K562	blood:	n/a	n/a
5	POLR2A	chr16:70605504-70611628	K562	blood:	n/a	n/a
6	POLR2A	chr16:70605669-70607070	K562	blood:	n/a	n/a
7	POLR2A	chr16:70605539-70612779	K562	blood:	n/a	n/a
8	POLR2A	chr16:70606080-70607086	K562	blood:	n/a	n/a
9	POLR2A	chr16:70605926-70607079	HL-60	blood:	n/a	n/a
10	POLR2A	chr16:70605962-70608025	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr16:70606395-70608623	K562	blood:	n/a	n/a
12	POLR2A	chr16:70605726-70607983	K562	blood:	n/a	n/a
13	POLR2A	chr16:70606497-70606696	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr16:70606433-70607911	Hela-S3	cervix:	n/a	n/a
15	GATA2	chr16:70606058-70608037	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr16:70605676-70608076	K562	blood:	n/a	n/a
17	POLR2A	chr16:70606088-70609006	HepG2	liver:	n/a	n/a
18	POLR2A	chr16:70606450-70607106	GM12892	blood:	n/a	n/a
19	POLR2A	chr16:70606313-70607993	HepG2	liver:	n/a	n/a
20	POLR2A	chr16:70605830-70608006	GM12891	blood:	n/a	n/a
21	POLR2A	chr16:70605838-70606567	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr16:70606148-70607151	K562	blood:	n/a	n/a
23	POLR2A	chr16:70605611-70607075	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr16:70606285-70606844	HepG2	liver:	n/a	n/a
25	POLR2A	chr16:70606134-70608011	GM12878	blood:	n/a	n/a
26	POLR2A	chr16:70606485-70607323	GM12892	blood:	n/a	n/a
27	POLR2A	chr16:70603398-70612236	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:70605757-70608578	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr16:70605834-70606518	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr16:70606411-70607070	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr16:70605764-70607152	HL-60	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70556571..70559588-chr16:70605085..70607867,3	MCF-7	breast:
2	chr16:70604065..70607054-chr16:70608889..70610552,2	K562	blood:
3	chr16:70603041..70604575-chr16:70605082..70606614,2	MCF-7	breast:
4	chr16:70601244..70603695-chr16:70604448..70607649,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260023	TF binding region
ENSG00000103051	Chromatin interaction
ENSG00000189091	Chromatin interaction
ENSG00000260023	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11075767	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs11075770	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs11643373	0.96[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs11645585	0.80[AMR][1000 genomes]
rs11648402	0.96[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs11649341	1.00[MKK][hapmap]
rs12597401	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs1551526	1.00[LWK][hapmap]
rs2168606	0.81[CHD][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs2288491	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs2303791	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3762171	0.88[MEX][hapmap]
rs4432264	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4436771	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs4985533	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4985534	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[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];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499317	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6499320	0.82[AMR][1000 genomes]
rs6499321	0.81[AMR][1000 genomes]
rs71401814	0.82[AMR][1000 genomes]
rs7200430	1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs7201750	0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs7204583	0.87[AMR][1000 genomes]
rs722579	0.88[MEX][hapmap]
rs8045651	0.80[AMR][1000 genomes]
rs8046881	0.86[AMR][1000 genomes]
rs8049641	0.92[MEX][hapmap];0.85[TSI][hapmap]
rs8049786	0.85[AMR][1000 genomes]
rs8051506	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs8052031	0.84[AMR][1000 genomes]
rs8052125	1.00[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs8057610	1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs8062178	0.80[AMR][1000 genomes]
rs875858	1.00[MKK][hapmap]
rs9929904	0.81[AMR][1000 genomes]
rs9936225	1.00[MEX][hapmap];0.80[TSI][hapmap]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7190039	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs7190039	COG4	cis	lymphoblastoid	seeQTL
rs7190039	PDPR	cis	cerebellum	SCAN
rs7190039	BEAN	cis	cerebellum	SCAN
rs7190039	EXOSC6	cis	parietal	SCAN
rs7190039	WWP2	cis	cerebellum	SCAN
rs7190039	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs7190039	C16orf86	cis	cerebellum	SCAN
rs7190039	SF3B3	cis	parietal	SCAN
rs7190039	CLEC18A	cis	Artery Aorta	GTEx
rs7190039	WWP2	cis	parietal	SCAN
rs7190039	SF3B3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70560400-70607800	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr16:70560600-70609600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:70560800-70608800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:70561000-70608800	Strong transcription	Fetal Thymus	thymus
5	chr16:70561000-70609000	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr16:70561000-70609400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr16:70561000-70610000	Strong transcription	Thymus	Thymus
8	chr16:70561200-70609400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr16:70561200-70609600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:70561400-70607600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:70561400-70609000	Strong transcription	Primary B cells from cord blood	blood
12	chr16:70561400-70610000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:70561600-70609000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr16:70561600-70609200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr16:70561600-70609600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr16:70561600-70609800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr16:70562200-70609600	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr16:70562800-70608800	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr16:70562800-70609000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:70563200-70606600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:70563200-70609000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr16:70563200-70609600	Strong transcription	Primary T cells from cord blood	blood
23	chr16:70563200-70609800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr16:70563200-70610000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr16:70563400-70608400	Strong transcription	Fetal Brain Female	brain
26	chr16:70563400-70609000	Strong transcription	Brain Anterior Caudate	brain
27	chr16:70563400-70609800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr16:70563400-70610000	Strong transcription	A549	lung
29	chr16:70563600-70607400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr16:70563600-70608200	Strong transcription	HepG2	liver
31	chr16:70563600-70609600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:70563800-70608600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr16:70563800-70610000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr16:70564000-70607800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:70564600-70608800	Strong transcription	Hela-S3	cervix
36	chr16:70566800-70608000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr16:70569400-70609000	Strong transcription	K562	blood
38	chr16:70570000-70609600	Strong transcription	Dnd41	blood
39	chr16:70570400-70608600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr16:70570800-70606600	Strong transcription	Colonic Mucosa	Colon
41	chr16:70571000-70608200	Strong transcription	GM12878-XiMat	blood
42	chr16:70571600-70607000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr16:70574600-70609800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr16:70574800-70607800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr16:70577600-70606600	Strong transcription	Brain Substantia Nigra	brain
46	chr16:70578000-70608400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr16:70581200-70609600	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr16:70581600-70611400	Strong transcription	Brain Germinal Matrix	brain
49	chr16:70581800-70608000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr16:70582400-70609000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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