Variant report

Variant	rs599316
Chromosome Location	chr15:42486757-42486758
allele	A/G
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	MAX	chr15:42486695-42487178	Hela-S3	cervix:	n/a	chr15:42486956-42486966
2	JUND	chr15:42486672-42487027	HepG2	liver:	n/a	chr15:42486871-42486882
3	FOS	chr15:42486713-42487099	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXP2	chr15:42486729-42486989	PFSK-1	brain:	n/a	n/a
5	JUND	chr15:42486726-42487063	K562	blood:	n/a	chr15:42486871-42486882
6	JUN	chr15:42486711-42487174	Hela-S3	cervix:	n/a	n/a
7	MAX	chr15:42486735-42487128	Hela-S3	cervix:	n/a	chr15:42486956-42486966
8	FOXA1	chr15:42486742-42487095	HepG2	liver:	n/a	n/a
9	FOSL2	chr15:42486661-42487079	HepG2	liver:	n/a	chr15:42486872-42486883
10	FOSL2	chr15:42486613-42487120	HepG2	liver:	n/a	chr15:42486872-42486883
11	CEBPB	chr15:42486668-42487078	MCF-7	breast:	n/a	chr15:42486881-42486892
12	SIN3AK20	chr15:42486708-42487284	MCF-7	breast:	n/a	n/a
13	EP300	chr15:42486751-42487192	HepG2	liver:	n/a	n/a
14	MYC	chr15:42486729-42487161	NB4	blood:	n/a	chr15:42486956-42486966
15	CEBPB	chr15:42486699-42487140	A549	lung:	n/a	chr15:42486881-42486892
16	STAT3	chr15:42486674-42486903	MCF10A-Er-Src	breast:	n/a	n/a
17	CEBPD	chr15:42486741-42486990	HepG2	liver:	n/a	n/a
18	CEBPB	chr15:42486696-42487134	IMR90	lung:	n/a	chr15:42486881-42486892
19	FOSL2	chr15:42486725-42486998	A549	lung:	n/a	chr15:42486872-42486883
20	E2F4	chr15:42486705-42487022	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr15:42486741-42486897	Hela-S3	cervix:	n/a	n/a
22	ATF3	chr15:42486677-42486975	K562	blood:	n/a	n/a
23	JUND	chr15:42486713-42487061	HepG2	liver:	n/a	chr15:42486871-42486882
24	JUN	chr15:42486631-42487445	K562	blood:	n/a	n/a
25	FOXA1	chr15:42486686-42487173	HepG2	liver:	n/a	n/a
26	CEBPB	chr15:42486689-42487143	A549	lung:	n/a	chr15:42486881-42486892
27	MYC	chr15:42486729-42487127	Hela-S3	cervix:	n/a	chr15:42486956-42486966
28	MAX	chr15:42486715-42487266	NB4	blood:	n/a	chr15:42486956-42486966
29	CEBPB	chr15:42486675-42487234	Hela-S3	cervix:	n/a	chr15:42486881-42486892
30	CHD2	chr15:42486743-42487067	Hela-S3	cervix:	n/a	n/a
31	MAX	chr15:42486566-42487224	HepG2	liver:	n/a	chr15:42486956-42486966
32	CEBPB	chr15:42486683-42487059	K562	blood:	n/a	chr15:42486881-42486892
33	USF2	chr15:42486733-42487086	Hela-S3	cervix:	n/a	n/a
34	CEBPD	chr15:42486638-42487131	K562	blood:	n/a	n/a
35	JUND	chr15:42486743-42486959	HepG2	liver:	n/a	chr15:42486871-42486882
36	RFX5	chr15:42486683-42487080	Hela-S3	cervix:	n/a	n/a
37	FOS	chr15:42486705-42487084	MCF10A-Er-Src	breast:	n/a	n/a
38	MXI1	chr15:42486745-42487185	Hela-S3	cervix:	n/a	n/a
39	EP300	chr15:42486726-42487151	Hela-S3	cervix:	n/a	n/a
40	FOS	chr15:42486705-42487089	MCF10A-Er-Src	breast:	n/a	n/a
41	FOSL2	chr15:42486672-42486972	MCF-7	breast:	n/a	chr15:42486872-42486883
42	CEBPD	chr15:42486755-42486939	HepG2	liver:	n/a	n/a
43	CEBPB	chr15:42486678-42487216	A549	lung:	n/a	chr15:42486881-42486892
44	FOXA1	chr15:42486685-42487025	HepG2	liver:	n/a	n/a
45	FOS	chr15:42486696-42487077	MCF10A-Er-Src	breast:	n/a	n/a
46	GTF2F1	chr15:42486746-42487042	Hela-S3	cervix:	n/a	n/a
47	MYC	chr15:42486719-42487153	MCF10A-Er-Src	breast:	n/a	chr15:42486956-42486966
48	MXI1	chr15:42486738-42487117	HepG2	liver:	n/a	n/a
49	JUND	chr15:42486690-42487192	Hela-S3	cervix:	n/a	chr15:42486871-42486882
50	CEBPB	chr15:42486703-42487152	HepG2	liver:	n/a	chr15:42486881-42486892

No.	Distal block	Cell Line	Cell type
1	chr15:42478640..42481738-chr15:42484434..42487278,4	K562	blood:
2	chr15:42443129..42444925-chr15:42485873..42487790,2	MCF-7	breast:
3	chr15:42482969..42485392-chr15:42485686..42487321,2	MCF-7	breast:

Variant related genes	Relation type
VPS39	TF binding region
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1626437	0.82[ASN][1000 genomes]
rs1678995	0.82[ASN][1000 genomes]
rs1678996	0.82[ASN][1000 genomes]
rs1679000	0.82[ASN][1000 genomes]
rs1679001	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1679008	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1703748	0.82[ASN][1000 genomes]
rs1703751	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1703753	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1712390	0.82[ASN][1000 genomes]
rs1712391	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1712407	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412671	0.82[ASN][1000 genomes]
rs2620378	0.82[ASN][1000 genomes]
rs2620379	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2620380	0.82[ASN][1000 genomes]
rs2663092	0.82[ASN][1000 genomes]
rs2677751	0.82[ASN][1000 genomes]
rs28767320	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2928333	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs583541	0.85[ASN][1000 genomes]
rs588695	0.85[ASN][1000 genomes]
rs590540	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs593910	0.82[ASN][1000 genomes]
rs598441	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs602270	0.82[ASN][1000 genomes]
rs609660	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs613131	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs613157	0.82[ASN][1000 genomes]
rs614733	0.82[ASN][1000 genomes]
rs614774	0.82[ASN][1000 genomes]
rs616071	0.82[ASN][1000 genomes]
rs621365	0.82[ASN][1000 genomes]
rs627478	0.82[ASN][1000 genomes]
rs629255	0.82[ASN][1000 genomes]
rs633483	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs635617	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs635669	0.82[ASN][1000 genomes]
rs635690	0.82[ASN][1000 genomes]
rs635919	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs636604	0.82[ASN][1000 genomes]
rs637445	0.82[ASN][1000 genomes]
rs641119	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs644627	0.82[ASN][1000 genomes]
rs645304	0.82[ASN][1000 genomes]
rs647581	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs650910	0.82[ASN][1000 genomes]
rs660033	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs663454	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs665262	0.82[ASN][1000 genomes]
rs665718	0.82[ASN][1000 genomes]
rs668973	0.82[ASN][1000 genomes]
rs670329	0.82[ASN][1000 genomes]
rs670421	0.82[ASN][1000 genomes]
rs672946	0.82[ASN][1000 genomes]
rs677845	0.82[ASN][1000 genomes]
rs677895	0.82[ASN][1000 genomes]
rs685521	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7181577	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs599316	LRRC57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42450600-42487400	Strong transcription	Primary B cells from cord blood	blood
2	chr15:42451000-42487600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:42451200-42487600	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:42460000-42499200	Weak transcription	A549	lung
5	chr15:42460000-42499800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:42466000-42498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:42475000-42499200	Weak transcription	Stomach Mucosa	stomach
8	chr15:42476800-42499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42477200-42497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:42477400-42487400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:42478400-42486800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:42478400-42498600	Weak transcription	Gastric	stomach
13	chr15:42480200-42496000	Weak transcription	Esophagus	oesophagus
14	chr15:42480400-42498600	Weak transcription	Small Intestine	intestine
15	chr15:42480400-42498800	Weak transcription	Right Ventricle	heart
16	chr15:42480600-42491400	Weak transcription	Psoas Muscle	Psoas
17	chr15:42480600-42496000	Weak transcription	Spleen	Spleen
18	chr15:42481200-42499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:42481400-42489600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:42481600-42497600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:42481600-42497600	Weak transcription	HUVEC	blood vessel
22	chr15:42481600-42498600	Weak transcription	Fetal Brain Male	brain
23	chr15:42482800-42499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:42483200-42499400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:42483400-42489600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:42483400-42498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:42483400-42498600	Weak transcription	Fetal Kidney	kidney
28	chr15:42483600-42497600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:42483600-42498600	Weak transcription	Brain Substantia Nigra	brain
30	chr15:42483600-42498600	Weak transcription	K562	blood
31	chr15:42483600-42499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:42483800-42489600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:42483800-42489600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:42483800-42489600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:42483800-42489600	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:42483800-42492600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:42483800-42499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:42484000-42489600	Weak transcription	Placenta	Placenta
39	chr15:42484000-42489800	Weak transcription	NHDF-Ad	bronchial
40	chr15:42484000-42499200	Weak transcription	HMEC	breast
41	chr15:42484200-42489600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:42484200-42490000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:42484200-42491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:42484200-42493400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:42484400-42486800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:42484400-42489600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:42484400-42489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr15:42484400-42489600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:42484400-42489600	Weak transcription	NH-A	brain
50	chr15:42484400-42489800	Weak transcription	HSMM	muscle

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