Variant report

Variant	rs11856413
Chromosome Location	chr15:75199892-75199893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr15:75198735-75200076	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75198218-75200012	K562	blood:	n/a	n/a
3	TEAD4	chr15:75198980-75199955	K562	blood:	n/a	n/a
4	POLR2A	chr15:75198142-75199971	K562	blood:	n/a	n/a
5	POLR2A	chr15:75197730-75200094	HepG2	liver:	n/a	n/a
6	BCL3	chr15:75198747-75199900	A549	lung:	n/a	chr15:75198876-75198889
7	POLR2A	chr15:75197907-75199946	PFSK-1	brain:	n/a	n/a
8	PML	chr15:75198431-75200041	GM12878	blood:	n/a	chr15:75198572-75198580
9	POLR2A	chr15:75198204-75199951	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr15:75198921-75200303	K562	blood:	n/a	n/a
11	HCFC1	chr15:75197757-75200452	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:75197995-75199934	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr15:75198506-75199964	K562	blood:	n/a	n/a
14	POLR2A	chr15:75198230-75200017	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr15:75198717-75199913	ECC-1	luminal epithelium:	n/a	n/a
16	TCF12	chr15:75198142-75200209	A549	lung:	n/a	n/a
17	POLR2A	chr15:75197869-75200093	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:75199837-75199907	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr15:75198332-75199940	PBDE	blood:	n/a	n/a
20	SIN3AK20	chr15:75198014-75200254	MCF-7	breast:	n/a	n/a
21	POLR2A	chr15:75197977-75200316	SK-N-MC	brain:	n/a	n/a
22	BCL3	chr15:75198697-75199923	A549	lung:	n/a	chr15:75198876-75198889
23	POLR2A	chr15:75198917-75200002	HCT-116	colon:	n/a	n/a
24	MXI1	chr15:75198076-75200393	IMR90	lung:	n/a	n/a
25	POLR2A	chr15:75198253-75199929	MCF-7	breast:	n/a	n/a
26	REST	chr15:75197828-75200077	H1-neurons	neurons:	n/a	chr15:75198719-75198732
27	POLR2A	chr15:75198802-75200061	K562	blood:	n/a	n/a
28	KAP1	chr15:75198996-75199937	HEK293	kidney:	n/a	n/a
29	MAZ	chr15:75198241-75200078	IMR90	lung:	n/a	chr15:75198506-75198515
30	POLR2A	chr15:75198919-75199931	K562	blood:	n/a	n/a
31	POLR2A	chr15:75198344-75199933	K562	blood:	n/a	n/a
32	POLR2A	chr15:75198164-75199927	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75133790..75137554-chr15:75195204..75200578,14	MCF-7	breast:
2	chr15:75199878..75202215-chr15:75221467..75223447,2	K562	blood:
3	chr15:75132852..75135633-chr15:75196341..75200571,3	K562	blood:
4	chr15:75073435..75075467-chr15:75197436..75200109,2	K562	blood:
5	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
6	chr15:75107985..75111072-chr15:75197111..75200997,5	MCF-7	breast:
7	chr15:75197919..75201119-chr15:75247045..75249740,3	K562	blood:
8	chr15:75197370..75200380-chr15:75247025..75249904,3	MCF-7	breast:
9	chr15:75199141..75199932-chr16:4897486..4898023,2	HCT-116	colon:
10	chr15:75191256..75201000-chr15:75228549..75233626,13	K562	blood:
11	chr15:75196237..75205947-chr15:75227299..75233104,18	K562	blood:
12	chr15:75199684..75201494-chr15:75226994..75229978,2	MCF-7	breast:
13	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
14	chr15:75196219..75200292-chr15:75228985..75231952,6	MCF-7	breast:

No data

Variant related genes	Relation type
FAM219B	TF binding region
ENSG00000261606	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000118900	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11072511	0.96[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11072512	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11072513	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072514	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1127796	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1130741	1.00[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1133322	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1133323	1.00[ASW][hapmap];0.96[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];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630087	0.80[AMR][1000 genomes]
rs11630592	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11630918	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633472	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636892	0.80[AMR][1000 genomes]
rs11638130	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11639413	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11854704	0.84[ASW][hapmap];0.96[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11857695	0.86[EUR][1000 genomes]
rs12148513	0.83[AFR][1000 genomes]
rs12487	0.84[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap]
rs12898539	0.82[AMR][1000 genomes]
rs12899787	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12900662	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12901190	1.00[ASW][hapmap];0.96[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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12902515	0.86[EUR][1000 genomes]
rs12903205	0.86[EUR][1000 genomes]
rs12903370	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904326	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904897	0.86[EUR][1000 genomes]
rs12907898	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908365	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12909335	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12911254	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912343	0.81[AMR][1000 genomes]
rs12912839	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913293	0.89[EUR][1000 genomes]
rs12914217	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1378942	1.00[LWK][hapmap]
rs2044157	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2168518	1.00[LWK][hapmap]
rs2290573	0.84[ASW][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap]
rs2415251	0.84[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34063670	0.81[AMR][1000 genomes]
rs34799293	0.80[AMR][1000 genomes]
rs35556055	0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs35882241	0.81[AMR][1000 genomes]
rs3812945	0.83[MEX][hapmap]
rs4643278	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886413	0.80[AMR][1000 genomes]
rs4886608	0.84[EUR][1000 genomes]
rs4886632	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886636	0.96[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs4886639	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886640	0.89[EUR][1000 genomes]
rs4886649	0.84[ASW][hapmap]
rs59945415	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62029167	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62029217	0.80[AMR][1000 genomes]
rs6495122	0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs7495664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7495739	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs7497026	0.85[EUR][1000 genomes]
rs7497393	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8025447	0.90[EUR][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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11856413	CYP1A1	cis	cerebellum	SCAN
rs11856413	SCAMP2	cis	parietal	SCAN
rs11856413	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs11856413	CSK	cis	lymphoblastoid	seeQTL
rs11856413	ULK3	cis	parietal	SCAN
rs11856413	TLE3	cis	cerebellum	SCAN
rs11856413	MPI	cis	lymphoblastoid	seeQTL
rs11856413	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs11856413	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs11856413	SCAMP2	cis	Whole Blood	GTEx
rs11856413	SCAMP5	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75197400-75200000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:75197800-75200000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:75197800-75200000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr15:75197800-75200200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:75198000-75200000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:75198200-75200000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:75198400-75200000	Flanking Active TSS	Colonic Mucosa	Colon
8	chr15:75199400-75200000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:75199400-75200000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr15:75199400-75200000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr15:75199400-75200000	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr15:75199400-75200000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr15:75199400-75200000	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr15:75199400-75200000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr15:75199400-75200000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:75199400-75200000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:75199400-75200000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:75199400-75200000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr15:75199400-75200000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:75199400-75200000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:75199400-75200000	Flanking Active TSS	Fetal Brain Male	brain
22	chr15:75199400-75200000	Flanking Active TSS	Placenta	Placenta
23	chr15:75199400-75200000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:75199400-75200000	Flanking Active TSS	GM12878-XiMat	blood
25	chr15:75199400-75200000	Flanking Active TSS	Hela-S3	cervix
26	chr15:75199400-75200000	Flanking Active TSS	HMEC	breast
27	chr15:75199400-75200000	Flanking Active TSS	HSMM	muscle
28	chr15:75199400-75200000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr15:75199400-75200000	Flanking Active TSS	NH-A	brain
30	chr15:75199400-75200000	Flanking Active TSS	NHEK	skin
31	chr15:75199400-75200200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:75199400-75200200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr15:75199400-75200200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:75199400-75200200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr15:75199400-75200200	Flanking Active TSS	Dnd41	blood
36	chr15:75199600-75200000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr15:75199600-75200000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr15:75199600-75200000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:75199600-75200000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr15:75199600-75200000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr15:75199600-75200000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:75199600-75200000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr15:75199600-75200000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:75199600-75200000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:75199600-75200000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:75199600-75200000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:75199600-75200000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr15:75199600-75200000	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr15:75199600-75200000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr15:75199600-75200000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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