Variant report

Variant	rs923828
Chromosome Location	chr12:58015494-58015495
allele	C/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	MYBL2	chr12:58015423-58016035	HepG2	liver:	n/a	n/a
2	CBX3	chr12:58015484-58015995	K562	blood:	n/a	n/a
3	BHLHE40	chr12:58014958-58016034	K562	blood:	n/a	n/a
4	RUNX3	chr12:58015458-58015879	GM12878	blood:	n/a	n/a
5	CTCF	chr12:58015424-58016034	A549	lung:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
6	HMGN3	chr12:58015312-58015861	K562	blood:	n/a	n/a
7	UBTF	chr12:58015460-58015980	K562	blood:	n/a	n/a
8	CTCF	chr12:58015459-58015944	NHEK	skin:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
9	FOXM1	chr12:58015435-58015898	GM12878	blood:	n/a	n/a
10	NRF1	chr12:58015368-58015965	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr12:58015483-58016030	H1-hESC	embryonic stem cell:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705
12	RAD21	chr12:58015374-58016053	H1-hESC	embryonic stem cell:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705
13	MAX	chr12:58014788-58015947	A549	lung:	n/a	n/a
14	CTCF	chr12:58015413-58016017	K562	blood:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
15	CTCF	chr12:58015381-58016064	GM19238	blood:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
16	CTCF	chr12:58015488-58015962	IMR90	lung:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
17	RUNX3	chr12:58015471-58015852	GM12878	blood:	n/a	n/a
18	CTBP2	chr12:58014471-58015792	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr12:58015085-58015716	A549	lung:	n/a	n/a
20	TEAD4	chr12:58015466-58015935	K562	blood:	n/a	n/a
21	RAD21	chr12:58015494-58015969	GM12878	blood:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705
22	MTA3	chr12:58015452-58015945	GM12878	blood:	n/a	n/a
23	ZNF263	chr12:58014941-58016756	HEK293-T-REx	kidney:	n/a	chr12:58015275-58015296 chr12:58015314-58015335
24	MAX	chr12:58014564-58015961	A549	lung:	n/a	n/a
25	JUND	chr12:58015482-58016093	K562	blood:	n/a	n/a
26	SUZ12	chr12:58012720-58016103	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr12:58015491-58015899	Fibrobl	skin:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
28	MYC	chr12:58015065-58015957	K562	blood:	n/a	n/a
29	CTCF	chr12:58015490-58016025	GM19240	blood:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
30	BCL3	chr12:58015173-58015794	A549	lung:	n/a	chr12:58015687-58015700 chr12:58015689-58015702
31	RAD21	chr12:58015489-58015993	ECC-1	luminal epithelium:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705
32	RAD21	chr12:58015254-58016068	A549	lung:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705
33	BHLHE40	chr12:58014987-58015846	HepG2	liver:	n/a	n/a
34	CTCF	chr12:58015438-58016018	GM12878	blood:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
35	MXI1	chr12:58014944-58015980	IMR90	lung:	n/a	n/a
36	CTCF	chr12:58015477-58016306	K562	blood:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
37	MAX	chr12:58014538-58015940	HepG2	liver:	n/a	n/a
38	ZBTB7A	chr12:58015360-58015943	ECC-1	luminal epithelium:	n/a	chr12:58015862-58015871
39	MAX	chr12:58014623-58015986	HepG2	liver:	n/a	n/a
40	RAD21	chr12:58015373-58015967	HepG2	liver:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705
41	CTCF	chr12:58015146-58016219	SK-N-SH	brain:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
42	CTCF	chr12:58015330-58016141	MCF-7	breast:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
43	CTCF	chr12:58015412-58016145	K562	blood:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
44	TCF12	chr12:58015464-58015860	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr12:58015434-58016010	H1-hESC	embryonic stem cell:	n/a	chr12:58015695-58015708 chr12:58015695-58015708 chr12:58015694-58015710 chr12:58015688-58015709 chr12:58015696-58015706 chr12:58015699-58015708 chr12:58015693-58015711
46	BACH1	chr12:58015395-58015949	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr12:58014885-58015917	K562	blood:	n/a	n/a
48	MAX	chr12:58015015-58015754	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:58014950-58016867	H1-neurons	neurons:	n/a	n/a
50	RAD21	chr12:58015483-58016017	IMR90	lung:	n/a	chr12:58015694-58015707 chr12:58015691-58015710 chr12:58015695-58015705

No.	Distal block	Cell Line	Cell type
1	chr12:58015127..58017483-chr12:58164900..58167382,2	K562	blood:
2	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
3	chr12:57908723..57911184-chr12:58015382..58017186,3	K562	blood:
4	chr12:57998188..58000440-chr12:58014339..58016922,2	MCF-7	breast:
5	chr12:58015100..58016862-chr12:58023977..58026856,2	MCF-7	breast:
6	chr12:57976942..57977694-chr12:58014849..58016025,6	MCF-7	breast:
7	chr12:57852790..57853327-chr12:58015168..58015867,2	MCF-7	breast:
8	chr12:58015255..58016233-chr12:58026528..58027063,5	K562	blood:
9	chr12:57912866..57916321-chr12:58013594..58015753,4	K562	blood:
10	chr12:58014906..58016961-chr12:58128240..58131170,2	K562	blood:
11	chr12:57911911..57916321-chr12:58013702..58018076,7	K562	blood:
12	chr12:57976679..57977833-chr12:58015073..58017142,20	MCF-7	breast:
13	chr12:57977834..57978565-chr12:58015492..58016047,2	MCF-7	breast:
14	chr12:57992028..57994332-chr12:58015405..58017173,2	MCF-7	breast:
15	chr12:58004734..58005360-chr12:58015231..58015962,2	K562	blood:
16	chr12:57913535..57914259-chr12:58015361..58016151,2	K562	blood:
17	chr12:57976760..57978150-chr12:58015081..58016157,16	K562	blood:

Variant related genes	Relation type
SLC26A10	TF binding region
ENSG00000224713	TF binding region
ENSG00000135454	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1027315	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1038914	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1050045	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs12368653	0.86[MEX][hapmap]
rs12371356	0.81[MEX][hapmap]
rs1552842	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564374	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873919	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277324	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277326	0.85[MEX][hapmap]
rs2307095	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2307097	0.85[MEX][hapmap]
rs2640610	0.85[ASN][1000 genomes]
rs7134861	0.81[ASN][1000 genomes]
rs7295422	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs7304145	0.89[ASN][1000 genomes]
rs7311632	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs7966795	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs799265	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs903067	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]

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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs923828	NCKAP1L	cis	parietal	SCAN
rs923828	FAM119B	cis	cerebellum	SCAN
rs923828	STAT6	cis	parietal	SCAN
rs923828	FAM119B	cis	lymphoblastoid	seeQTL
rs923828	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs923828	OR6C4	cis	cerebellum	SCAN
rs923828	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs923828	TSPAN31	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58011600-58018000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58011800-58018800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:58012000-58019000	Weak transcription	Aorta	Aorta
4	chr12:58013000-58016000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:58014200-58015800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:58014400-58015600	Bivalent Enhancer	Spleen	Spleen
7	chr12:58014600-58015600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr12:58014600-58015600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
9	chr12:58014600-58015600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
10	chr12:58014600-58015800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:58014600-58015800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr12:58014600-58015800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
13	chr12:58014600-58015800	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
14	chr12:58014600-58015800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:58014600-58015800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
16	chr12:58014600-58015800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
17	chr12:58014600-58015800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr12:58014600-58016000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr12:58014600-58016000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:58014600-58016000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr12:58014600-58016000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr12:58014600-58016000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:58014600-58016000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:58014600-58016000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:58014600-58016000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:58014600-58016000	Bivalent Enhancer	Fetal Thymus	thymus
27	chr12:58014600-58016000	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr12:58014800-58015600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
29	chr12:58014800-58015600	Enhancers	Gastric	stomach
30	chr12:58014800-58015600	Bivalent/Poised TSS	A549	lung
31	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
33	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
34	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
35	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
44	chr12:58014800-58015800	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr12:58014800-58015800	Flanking Active TSS	Right Atrium	heart
46	chr12:58014800-58015800	Flanking Active TSS	Right Ventricle	heart
47	chr12:58014800-58015800	Flanking Bivalent TSS/Enh	NHEK	skin
48	chr12:58014800-58016000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:58014800-58016000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:58014800-58016000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon

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