Variant report

Variant	rs12933210
Chromosome Location	chr16:69742048-69742049
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69740530-69743833	MCF-7	breast:	n/a	n/a
2	POLR2A	chr16:69741274-69743842	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:69741755-69742876	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:69741607-69742838	K562	blood:	n/a	n/a
5	POLR2A	chr16:69741753-69742969	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr16:69741845-69742143	Hela-S3	cervix:	n/a	n/a
7	TCF12	chr16:69741156-69742211	A549	lung:	n/a	n/a
8	POLR2A	chr16:69741864-69742240	A549	lung:	n/a	n/a
9	POLR2A	chr16:69741809-69742176	HCT-116	colon:	n/a	n/a
10	POLR2A	chr16:69741704-69742086	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr16:69739930-69743902	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:69741895-69742192	A549	lung:	n/a	n/a
13	POLR2A	chr16:69741738-69742220	GM12891	blood:	n/a	n/a
14	POLR2A	chr16:69739832-69743980	A549	lung:	n/a	n/a
15	POLR2A	chr16:69741583-69742128	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr16:69741801-69742718	HepG2	liver:	n/a	n/a
17	MAX	chr16:69741742-69742248	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr16:69741937-69742076	K562	blood:	n/a	n/a
19	JUND	chr16:69741814-69742588	A549	lung:	n/a	n/a
20	POLR2A	chr16:69740169-69742240	HCT-116	colon:	n/a	n/a
21	POLR2A	chr16:69742028-69742129	HUVEC	blood vessel:	n/a	n/a
22	BCL3	chr16:69740012-69743000	A549	lung:	n/a	n/a
23	POLR2A	chr16:69741914-69742133	Hela-S3	cervix:	n/a	n/a
24	MAX	chr16:69741800-69742151	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr16:69741892-69742129	A549	lung:	n/a	n/a
26	BCL3	chr16:69741336-69742227	A549	lung:	n/a	n/a
27	POLR2A	chr16:69741616-69742205	HUVEC	blood vessel:	n/a	n/a
28	FOSL2	chr16:69741824-69743133	HepG2	liver:	n/a	n/a
29	POLR2A	chr16:69741600-69742098	HepG2	liver:	n/a	n/a
30	ELF1	chr16:69741666-69742060	A549	lung:	n/a	n/a
31	POLR2A	chr16:69741916-69742078	A549	lung:	n/a	n/a
32	POLR2A	chr16:69741859-69742090	HepG2	liver:	n/a	n/a
33	POLR2A	chr16:69741746-69742228	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69741680..69751385-chr16:69755023..69763559,18	MCF-7	breast:
2	chr16:69739781..69742163-chr16:69797369..69799073,2	MCF-7	breast:
3	chr16:69741307..69747044-chr16:69787229..69790189,11	MCF-7	breast:
4	chr16:69730798..69733637-chr16:69740516..69742330,2	MCF-7	breast:
5	chr16:69734561..69737941-chr16:69738671..69742586,5	MCF-7	breast:
6	chr16:69740285..69743443-chr16:69794568..69797700,3	MCF-7	breast:
7	chr16:69739403..69742355-chr16:69743812..69745961,3	MCF-7	breast:
8	chr16:69741703..69743553-chr16:69758543..69761964,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261602	TF binding region
ENSG00000141101	Chromatin interaction
ENSG00000198373	Chromatin interaction
ENSG00000181019	Chromatin interaction
ENSG00000260772	Chromatin interaction
ENSG00000262136	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11640319	0.84[ASN][1000 genomes]
rs12918548	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12921782	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12924052	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1469908	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1837016	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2017448	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2917670	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917671	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917678	0.82[ASN][1000 genomes]
rs2965749	0.82[ASN][1000 genomes]
rs3811348	0.80[EUR][1000 genomes]
rs3848278	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs45488899	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4633710	0.84[ASN][1000 genomes]
rs55780735	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499241	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7187634	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189878	0.80[AMR][1000 genomes]
rs7191292	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7192380	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8045432	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8049728	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8055756	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8061052	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9938213	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12933210	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:69726000-69755800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
4	chr16:69726800-69747600	Weak transcription	Fetal Heart	heart
5	chr16:69728200-69746200	Weak transcription	Stomach Mucosa	stomach
6	chr16:69728200-69758600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr16:69728400-69744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:69728400-69748800	Weak transcription	Gastric	stomach
9	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:69728600-69752000	Weak transcription	Fetal Brain Male	brain
11	chr16:69729200-69745000	Weak transcription	Spleen	Spleen
12	chr16:69729400-69743600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr16:69729400-69744800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr16:69729400-69745000	Weak transcription	Pancreas	Pancrea
15	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
16	chr16:69729400-69760000	Weak transcription	Ovary	ovary
17	chr16:69729600-69745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:69729800-69746200	Weak transcription	Aorta	Aorta
19	chr16:69729800-69746200	Weak transcription	Left Ventricle	heart
20	chr16:69729800-69748800	Weak transcription	Esophagus	oesophagus
21	chr16:69730000-69743400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr16:69730000-69743400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr16:69730000-69743600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr16:69730000-69745200	Weak transcription	Thymus	Thymus
25	chr16:69730000-69745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:69730000-69759000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr16:69730200-69742600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr16:69730200-69743400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr16:69730200-69743400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr16:69730200-69746000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:69730400-69744800	Weak transcription	Colonic Mucosa	Colon
32	chr16:69730400-69747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:69730600-69743600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
35	chr16:69730800-69744600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr16:69731000-69746000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:69731600-69743600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:69731800-69744400	Weak transcription	K562	blood
40	chr16:69731800-69745000	Weak transcription	Hela-S3	cervix
41	chr16:69731800-69746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
44	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart
45	chr16:69732000-69743400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr16:69732000-69746200	Weak transcription	Brain Substantia Nigra	brain
47	chr16:69732600-69743400	Weak transcription	Dnd41	blood
48	chr16:69732600-69744800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:69732600-69745000	Weak transcription	Fetal Thymus	thymus
50	chr16:69733000-69744800	Weak transcription	Fetal Muscle Trunk	muscle

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