Variant report

Variant	rs954326
Chromosome Location	chr12:48394823-48394824
allele	A/C
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	CTCF	chr12:48394780-48394930	A549	lung:	n/a	n/a
2	SMARCB1	chr12:48394643-48396159	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr12:48394821-48395565	Hela-S3	cervix:	n/a	n/a
4	MAFK	chr12:48394799-48395336	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr12:48394773-48395269	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr12:48394740-48394890	MCF-7	breast:	n/a	n/a
7	MAX	chr12:48394684-48396207	ECC-1	luminal epithelium:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948 chr12:48395771-48395781
8	CTCF	chr12:48394780-48394930	MCF-7	breast:	n/a	n/a
9	FOS	chr12:48394813-48395084	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr12:48394720-48394870	SAEC	small airway:	n/a	n/a
11	MAX	chr12:48394684-48395560	Hela-S3	cervix:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
12	SMC3	chr12:48394748-48395567	Hela-S3	cervix:	n/a	n/a
13	MAX	chr12:48394809-48394972	K562	blood:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
14	USF2	chr12:48394767-48395244	Hela-S3	cervix:	n/a	n/a
15	MAX	chr12:48394706-48395286	MCF-7	breast:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
16	GTF2F1	chr12:48394686-48395275	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr12:48394800-48394950	HUVEC	blood vessel:	n/a	n/a
18	MYC	chr12:48394758-48395121	H1-hESC	embryonic stem cell:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
19	POLR2A	chr12:48394703-48395086	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr12:48394760-48394910	HCPEpiC	choroid plexus:	n/a	n/a
21	CTCF	chr12:48394720-48394870	NHDF-neo	bronchial:	n/a	n/a
22	CTCF	chr12:48394820-48394970	HBMEC	blood vessel:	n/a	n/a
23	CTCF	chr12:48394780-48394930	AG10803	skin:	n/a	n/a
24	CTCF	chr12:48394780-48394930	NHEK	skin:	n/a	n/a
25	POLR2A	chr12:48394677-48395085	H1-neurons	neurons:	n/a	n/a
26	CHD2	chr12:48394741-48395793	Hela-S3	cervix:	n/a	n/a
27	HA-E2F1	chr12:48394653-48395663	MCF-7	breast:	n/a	chr12:48395408-48395417 chr12:48395378-48395392 chr12:48395422-48395432
28	TEAD4	chr12:48394633-48395104	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF1	chr12:48394734-48395094	H1-hESC	embryonic stem cell:	n/a	n/a
30	BRCA1	chr12:48394802-48395428	Hela-S3	cervix:	n/a	n/a
31	TCF7L2	chr12:48394816-48395527	Hela-S3	cervix:	n/a	n/a
32	RAD21	chr12:48394748-48395197	Hela-S3	cervix:	n/a	chr12:48395118-48395125
33	MAX	chr12:48394626-48395927	HCT-116	colon:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948 chr12:48395771-48395781
34	USF2	chr12:48394771-48395114	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr12:48394776-48394999	SK-N-SH_RA	brain:	n/a	n/a
36	HDAC2	chr12:48394644-48396832	MCF-7	breast:	n/a	n/a
37	CTCF	chr12:48394780-48394930	HPAF	blood vessel:	n/a	n/a
38	TEAD4	chr12:48394677-48394996	H1-hESC	embryonic stem cell:	n/a	n/a
39	SIN3A	chr12:48394675-48396247	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr12:48394740-48394890	AG09309	skin:	n/a	n/a
41	CTCF	chr12:48394780-48394930	AG04450	lung:	n/a	n/a
42	MAX	chr12:48394761-48395023	NB4	blood:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
43	CTCF	chr12:48394800-48394950	BJ	skin:	n/a	n/a
44	CTCF	chr12:48394720-48394870	HVMF	connective:	n/a	n/a
45	MAX	chr12:48394702-48395510	Hela-S3	cervix:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
46	POLR2A	chr12:48394761-48394994	Hela-S3	cervix:	n/a	n/a
47	RAD21	chr12:48394537-48395037	H1-hESC	embryonic stem cell:	n/a	chr12:48394649-48394662
48	MYC	chr12:48394709-48395592	MCF10A-Er-Src	breast:	n/a	chr12:48394935-48394950 chr12:48394938-48394949 chr12:48394940-48394947 chr12:48394939-48394949 chr12:48394937-48394952 chr12:48394938-48394949 chr12:48394939-48394948 chr12:48394939-48394949 chr12:48394939-48394948
49	USF1	chr12:48394727-48395039	SK-N-SH_RA	brain:	n/a	n/a
50	MXI1	chr12:48394775-48395558	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48298685..48300649-chr12:48393830..48395808,2	MCF-7	breast:
2	chr12:48297374..48299237-chr12:48393563..48396184,2	MCF-7	breast:
3	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:
4	chr12:48355944..48359601-chr12:48393326..48397759,4	MCF-7	breast:
5	chr12:48375572..48377835-chr12:48392669..48394961,2	MCF-7	breast:
6	chr12:48393217..48395308-chr12:48444642..48446730,2	MCF-7	breast:
7	chr12:48360987..48363483-chr12:48393695..48396604,4	MCF-7	breast:
8	chr12:48393252..48397718-chr12:48414474..48419166,5	MCF-7	breast:
9	chr12:48393914..48396723-chr12:48402943..48405805,2	K562	blood:
10	chr12:48342574..48344961-chr12:48394535..48396923,2	MCF-7	breast:
11	chr12:48356300..48358721-chr12:48393251..48396453,4	MCF-7	breast:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000257955	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000257985	Chromatin interaction
ENSG00000139219	Chromatin interaction
ENSG00000258203	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1049392	0.94[JPT][hapmap]
rs10747529	0.94[JPT][hapmap]
rs10875733	0.94[JPT][hapmap]
rs10875739	0.94[JPT][hapmap]
rs10875752	0.94[JPT][hapmap]
rs10875754	0.94[JPT][hapmap]
rs10875761	0.94[JPT][hapmap]
rs10875766	0.94[JPT][hapmap]
rs11168350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168353	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap]
rs11168354	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11168358	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11168363	0.94[JPT][hapmap]
rs11168364	0.94[JPT][hapmap]
rs11168373	0.93[JPT][hapmap]
rs11168404	0.94[JPT][hapmap]
rs11168417	0.94[JPT][hapmap]
rs11168424	0.94[JPT][hapmap]
rs11168434	0.94[JPT][hapmap]
rs11168435	0.94[JPT][hapmap]
rs11168438	0.91[JPT][hapmap]
rs11168445	0.93[JPT][hapmap]
rs11168448	0.94[JPT][hapmap]
rs11168453	0.94[JPT][hapmap]
rs11168454	0.94[JPT][hapmap]
rs12422355	0.94[JPT][hapmap]
rs12423250	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs17122567	0.90[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs1793958	0.83[JPT][hapmap];0.81[LWK][hapmap]
rs1793960	0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs1859442	0.81[ASN][1000 genomes]
rs1859443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2286020	0.94[JPT][hapmap]
rs2408954	0.94[JPT][hapmap]
rs3742075	0.86[JPT][hapmap]
rs3825403	0.94[JPT][hapmap]
rs4258439	0.94[JPT][hapmap]
rs7299704	0.94[JPT][hapmap]
rs7302354	0.94[JPT][hapmap]
rs7303677	0.94[JPT][hapmap]
rs7484942	0.94[JPT][hapmap]
rs765260	0.94[JPT][hapmap]
rs7962390	0.94[JPT][hapmap]
rs7962569	0.87[JPT][hapmap]
rs8181670	0.94[JPT][hapmap]
rs886589	0.94[JPT][hapmap]
rs9651981	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs9669263	0.97[ASN][1000 genomes]
rs9804751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs954326	C12orf68	cis	parietal	SCAN
rs954326	TMEM106C	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48390000-48395000	Weak transcription	Right Atrium	heart
2	chr12:48394000-48395000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48394200-48395000	Bivalent Enhancer	Fetal Intestine Small	intestine
4	chr12:48394200-48396000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:48394400-48395000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
6	chr12:48394600-48395000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr12:48394600-48395000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:48394600-48395000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:48394600-48395000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48394600-48395000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr12:48394600-48395000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr12:48394600-48395000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:48394600-48395000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:48394600-48395000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:48394600-48395000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:48394600-48395000	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr12:48394600-48395000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr12:48394600-48395000	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr12:48394600-48395000	Enhancers	Placenta	Placenta
20	chr12:48394600-48395000	Bivalent Enhancer	Fetal Stomach	stomach
21	chr12:48394600-48395000	Enhancers	Left Ventricle	heart
22	chr12:48394600-48395000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr12:48394600-48395000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
24	chr12:48394600-48395000	Enhancers	Right Ventricle	heart
25	chr12:48394600-48395000	Bivalent Enhancer	NHLF	lung
26	chr12:48394600-48395200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr12:48394600-48395200	Enhancers	Pancreas	Pancrea
28	chr12:48394600-48395200	Flanking Active TSS	Hela-S3	cervix
29	chr12:48394600-48395200	Flanking Active TSS	NHEK	skin
30	chr12:48394600-48395400	Bivalent Enhancer	Primary T cells from cord blood	blood
31	chr12:48394600-48395400	Flanking Active TSS	HMEC	breast
32	chr12:48394600-48395600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:48394600-48395800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:48394600-48396000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:48394600-48396200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr12:48394800-48395000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr12:48394800-48395000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:48394800-48395000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr12:48394800-48395000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:48394800-48395000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:48394800-48395000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:48394800-48395000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:48394800-48395000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:48394800-48395000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:48394800-48395000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:48394800-48395000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:48394800-48395000	Bivalent Enhancer	Brain Anterior Caudate	brain
48	chr12:48394800-48395000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr12:48394800-48395000	Bivalent Enhancer	Brain Hippocampus Middle	brain
50	chr12:48394800-48395000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain

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