Variant report

Variant	rs62109425
Chromosome Location	chr2:20212942-20212943
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	HDAC2	chr2:20212028-20213272	HepG2	liver:	n/a	chr2:20212924-20212938 chr2:20212921-20212935 chr2:20212926-20212940 chr2:20212917-20212931 chr2:20212920-20212934 chr2:20212925-20212939
2	TEAD4	chr2:20212283-20213452	HepG2	liver:	n/a	n/a
3	REST	chr2:20212729-20213197	HepG2	liver:	n/a	chr2:20213066-20213079
4	HEY1	chr2:20211853-20212959	HepG2	liver:	n/a	chr2:20211886-20211901
5	MAX	chr2:20211686-20213307	A549	lung:	n/a	n/a
6	ZBTB7A	chr2:20212319-20213092	ECC-1	luminal epithelium:	n/a	n/a
7	SIN3A	chr2:20211979-20213337	H1-hESC	embryonic stem cell:	n/a	n/a
8	NR3C1	chr2:20212366-20213341	A549	lung:	n/a	chr2:20213072-20213086 chr2:20213071-20213087 chr2:20213071-20213086 chr2:20213069-20213090 chr2:20213071-20213087 chr2:20213071-20213087 chr2:20213071-20213087 chr2:20213072-20213086 chr2:20213071-20213088
9	FOXA2	chr2:20212757-20213227	HepG2	liver:	n/a	n/a
10	HEY1	chr2:20212323-20212964	HepG2	liver:	n/a	n/a
11	FOXA1	chr2:20212290-20213320	HepG2	liver:	n/a	n/a
12	FOXA1	chr2:20212317-20213341	HepG2	liver:	n/a	n/a
13	MAX	chr2:20212353-20212959	A549	lung:	n/a	n/a
14	EP300	chr2:20212897-20213194	HepG2	liver:	n/a	chr2:20212923-20212937 chr2:20212921-20212935
15	CEBPB	chr2:20212498-20212957	H1-hESC	embryonic stem cell:	n/a	n/a
16	NFIC	chr2:20212459-20213294	HepG2	liver:	n/a	n/a
17	FOXA1	chr2:20212704-20213314	HepG2	liver:	n/a	n/a
18	MYBL2	chr2:20212461-20213641	HepG2	liver:	n/a	n/a
19	EP300	chr2:20212720-20213265	HepG2	liver:	n/a	chr2:20212923-20212937 chr2:20212921-20212935
20	HDAC2	chr2:20212339-20213087	HepG2	liver:	n/a	chr2:20212924-20212938 chr2:20212921-20212935 chr2:20212926-20212940 chr2:20212917-20212931 chr2:20212920-20212934 chr2:20212925-20212939
21	TCF7L2	chr2:20212924-20213264	HepG2	liver:	n/a	chr2:20213096-20213103 chr2:20213093-20213103
22	POLR2A	chr2:20211552-20213412	H1-hESC	embryonic stem cell:	n/a	n/a
23	NR3C1	chr2:20212876-20213276	A549	lung:	n/a	chr2:20213072-20213086 chr2:20213071-20213087 chr2:20213071-20213086 chr2:20213069-20213090 chr2:20213071-20213087 chr2:20213071-20213087 chr2:20213071-20213087 chr2:20213072-20213086 chr2:20213071-20213088
24	FOXA1	chr2:20212756-20213328	HepG2	liver:	n/a	n/a
25	MYBL2	chr2:20212462-20213431	HepG2	liver:	n/a	n/a
26	MAX	chr2:20211861-20212942	A549	lung:	n/a	n/a
27	MAZ	chr2:20211930-20213076	IMR90	lung:	n/a	n/a
28	SP1	chr2:20212787-20213336	HepG2	liver:	n/a	n/a
29	NFIC	chr2:20212436-20213342	HepG2	liver:	n/a	n/a
30	EP300	chr2:20212317-20213285	HepG2	liver:	n/a	chr2:20212923-20212937 chr2:20212921-20212935
31	ZBTB7A	chr2:20212929-20213252	HepG2	liver:	n/a	n/a
32	MAX	chr2:20211720-20213557	HepG2	liver:	n/a	n/a
33	MBD4	chr2:20212918-20213624	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20188544..20190994-chr2:20211302..20213941,2	MCF-7	breast:
2	chr2:20212605..20214922-chr2:20216980..20220655,3	MCF-7	breast:
3	chr2:20212620..20214988-chr2:20250395..20252051,2	MCF-7	breast:
4	chr2:20196234..20199275-chr2:20211073..20214096,3	MCF-7	breast:
5	chr11:356190..356865-chr2:20212456..20212956,2	MCF-7	breast:
6	chr2:20187710..20189541-chr2:20212607..20214933,2	K562	blood:
7	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
8	chr2:20187189..20189541-chr2:20212582..20214933,2	K562	blood:

Variant related genes	Relation type
MATN3	TF binding region
ENSG00000223734	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000227210	Chromatin interaction
ENSG00000118965	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10856792	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11096633	0.81[EUR][1000 genomes]
rs1147110	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11903882	0.81[EUR][1000 genomes]
rs12475660	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2006707	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs936509	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3327327	chr2:20211296-20213844	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv3393710	chr2:20211621-20213469	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62109425	TTC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20211400-20213200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:20211600-20213000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:20211600-20213000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:20211800-20213000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:20211800-20213000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:20211800-20213000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
7	chr2:20211800-20213000	Active TSS	HSMM	muscle
8	chr2:20211800-20213200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:20211800-20213200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:20211800-20213200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:20211800-20213200	Enhancers	Fetal Heart	heart
12	chr2:20211800-20213200	Enhancers	Spleen	Spleen
13	chr2:20212000-20213000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr2:20212000-20213000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr2:20212000-20213000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:20212000-20213000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:20212000-20213000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:20212000-20213000	Active TSS	Colon Smooth Muscle	Colon
19	chr2:20212000-20213000	Bivalent/Poised TSS	Fetal Stomach	stomach
20	chr2:20212000-20213000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr2:20212000-20213000	Active TSS	Rectal Smooth Muscle	rectum
22	chr2:20212000-20213000	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr2:20212000-20213000	Active TSS	NH-A	brain
24	chr2:20212000-20213200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr2:20212000-20213200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:20212000-20213200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:20212000-20213400	Enhancers	Placenta	Placenta
28	chr2:20212200-20213000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20212200-20213000	Active TSS	Brain Anterior Caudate	brain
30	chr2:20212200-20213000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr2:20212200-20213000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:20212200-20213000	Active TSS	Brain Substantia Nigra	brain
33	chr2:20212200-20213000	Active TSS	Ovary	ovary
34	chr2:20212200-20213000	Active TSS	NHLF	lung
35	chr2:20212200-20213200	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr2:20212400-20213000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:20212400-20213000	Flanking Active TSS	Liver	Liver
38	chr2:20212400-20213000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
39	chr2:20212400-20213200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr2:20212600-20213000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:20212600-20213000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:20212600-20213000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
43	chr2:20212600-20213000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr2:20212600-20213000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
45	chr2:20212600-20213000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
46	chr2:20212600-20213000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:20212600-20213000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
48	chr2:20212600-20213000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
49	chr2:20212600-20213000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr2:20212600-20213000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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