Variant report

Variant	rs523476
Chromosome Location	chr3:119395662-119395663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:117)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:117 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr3:119395561-119395761	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr3:119395636-119396818	A549	lung:	n/a	n/a
3	POLR2A	chr3:119394854-119396781	U87	brain:	n/a	n/a
4	POLR2A	chr3:119395196-119396925	U87	brain:	n/a	n/a
5	POLR2A	chr3:119394473-119396840	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:119395465-119395815	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:119394816-119396770	GM19099	blood:	n/a	n/a
8	POLR2A	chr3:119394983-119395805	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:119395538-119396719	GM19193	blood:	n/a	n/a
10	ELF1	chr3:119395645-119396755	MCF-7	breast:	n/a	chr3:119396258-119396269 chr3:119396236-119396245
11	GATA1	chr3:119394665-119396732	PBDE	blood:	n/a	chr3:119395225-119395236
12	SIN3A	chr3:119395459-119396622	H1-hESC	embryonic stem cell:	n/a	chr3:119396002-119396015
13	TBP	chr3:119395597-119395838	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr3:119395633-119395833	MCF10A-Er-Src	breast:	n/a	n/a
15	MAZ	chr3:119395503-119396646	K562	blood:	n/a	n/a
16	MAX	chr3:119395568-119396666	NB4	blood:	n/a	n/a
17	POLR2A	chr3:119395547-119396591	HepG2	liver:	n/a	n/a
18	ZMIZ1	chr3:119395650-119396406	K562	blood:	n/a	n/a
19	POLR2A	chr3:119394618-119396838	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:119395491-119396753	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:119395521-119396697	GM18526	blood:	n/a	n/a
22	POLR2A	chr3:119395196-119396986	U87	brain:	n/a	n/a
23	POLR2A	chr3:119394507-119396828	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:119395571-119395853	K562	blood:	n/a	n/a
25	POLR2A	chr3:119395566-119395834	Hela-S3	cervix:	n/a	n/a
26	TBL1XR1	chr3:119395592-119396693	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:119394772-119396781	U87	brain:	n/a	n/a
28	RUNX3	chr3:119395455-119396881	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:119395610-119396414	IMR90	lung:	n/a	n/a
30	POLR2A	chr3:119395545-119396629	K562	blood:	n/a	n/a
31	NR2C2	chr3:119395662-119396537	Hela-S3	cervix:	n/a	chr3:119395960-119395975 chr3:119395939-119395954
32	POLR2A	chr3:119395262-119395824	GM12891	blood:	n/a	n/a
33	RAD21	chr3:119395562-119395786	Hela-S3	cervix:	n/a	n/a
34	NR2F2	chr3:119395660-119396751	HepG2	liver:	n/a	chr3:119395960-119395975 chr3:119395939-119395954
35	NR2C2	chr3:119395647-119396553	HepG2	liver:	n/a	chr3:119395960-119395975 chr3:119395939-119395954
36	STAT3	chr3:119395623-119395823	MCF10A-Er-Src	breast:	n/a	n/a
37	MYC	chr3:119395648-119396831	NB4	blood:	n/a	n/a
38	RELA	chr3:119395567-119396684	GM18951	blood:	n/a	n/a
39	NR2F2	chr3:119395610-119396616	MCF-7	breast:	n/a	chr3:119395960-119395975 chr3:119395939-119395954
40	POLR2A	chr3:119394788-119396746	GM18505	blood:	n/a	n/a
41	POLR2A	chr3:119395611-119396588	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:119395602-119396695	GM15510	blood:	n/a	n/a
43	POLR2A	chr3:119394681-119396716	K562	blood:	n/a	n/a
44	NFATC1	chr3:119395127-119395832	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:119395377-119396762	PBDE	blood:	n/a	n/a
46	MAZ	chr3:119395616-119396568	Hela-S3	cervix:	n/a	n/a
47	WRNIP1	chr3:119395649-119395799	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:119395574-119396722	NB4	blood:	n/a	n/a
49	RAD21	chr3:119395580-119396553	IMR90	lung:	n/a	chr3:119396340-119396349
50	MXI1	chr3:119395567-119396621	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119181316..119183992-chr3:119395288..119397711,2	MCF-7	breast:
2	chr3:119217361..119219124-chr3:119394788..119396855,3	MCF-7	breast:
3	chr3:119371437..119373754-chr3:119392688..119396112,3	K562	blood:
4	chr3:119383202..119386543-chr3:119393770..119396267,3	MCF-7	breast:
5	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
6	chr3:119181523..119183291-chr3:119394912..119396579,2	MCF-7	breast:
7	chr3:119215767..119217677-chr3:119394561..119396315,2	MCF-7	breast:
8	chr3:119297880..119300098-chr3:119394986..119397161,3	MCF-7	breast:
9	chr3:119393569..119396281-chr3:119421855..119424087,2	MCF-7	breast:
10	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
11	chr3:119394727..119396286-chr3:119814089..119815777,2	K562	blood:
12	chr3:119383346..119386464-chr3:119395342..119399056,3	K562	blood:

No data

Variant related genes	Relation type
COX17	TF binding region
ENSG00000113845	Chromatin interaction
ENSG00000272967	Chromatin interaction
ENSG00000144843	Chromatin interaction
ENSG00000121577	Chromatin interaction
ENSG00000183833	Chromatin interaction
ENSG00000241155	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11720605	0.92[EUR][1000 genomes]
rs11914676	0.85[JPT][hapmap]
rs11923223	0.86[JPT][hapmap]
rs12490779	0.81[JPT][hapmap]
rs13062540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065543	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13065893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1317259	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830291	0.85[JPT][hapmap]
rs1872432	0.85[JPT][hapmap]
rs1880040	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1880041	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046430	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280578	0.85[JPT][hapmap]
rs2629395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2629397	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2629409	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670296	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688629	0.85[JPT][hapmap]
rs2688631	0.85[JPT][hapmap]
rs2688633	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2692618	0.88[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2698282	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3749417	0.95[ASN][1000 genomes]
rs3772134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687871	0.92[ASN][1000 genomes]
rs4688023	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4688024	0.85[JPT][hapmap]
rs484809	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs540420	0.81[JPT][hapmap]
rs552244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs572119	0.85[JPT][hapmap]
rs62265884	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6438541	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438542	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766563	0.90[JPT][hapmap]
rs6782253	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785698	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794484	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6794579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797667	0.90[YRI][hapmap]
rs6803814	0.80[JPT][hapmap]
rs6807079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693397	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613999	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626940	0.90[JPT][hapmap]
rs7633444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8007	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs940181	0.82[AMR][1000 genomes];0.92[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription 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	12 gene(s)	inside rSNPs	diseases
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs523476	POPDC2	cis	multi-tissue	Pritchard
rs523476	POPDC2	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119394600-119395800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:119394600-119396600	Active TSS	Left Ventricle	heart
3	chr3:119394800-119395800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr3:119394800-119395800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr3:119394800-119395800	Flanking Active TSS	Liver	Liver
6	chr3:119394800-119395800	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr3:119394800-119395800	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr3:119394800-119395800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr3:119394800-119396600	Active TSS	GM12878-XiMat	blood
10	chr3:119394800-119396800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:119394800-119396800	Active TSS	Colonic Mucosa	Colon
12	chr3:119394800-119396800	Active TSS	Psoas Muscle	Psoas
13	chr3:119394800-119396800	Active TSS	Right Ventricle	heart
14	chr3:119395000-119395800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr3:119395000-119395800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr3:119395000-119395800	Flanking Active TSS	Fetal Kidney	kidney
17	chr3:119395000-119395800	Flanking Active TSS	Fetal Stomach	stomach
18	chr3:119395000-119395800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr3:119395000-119395800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:119395000-119396000	Active TSS	Right Atrium	heart
21	chr3:119395000-119396400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:119395000-119396400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:119395000-119396400	Active TSS	Fetal Heart	heart
24	chr3:119395000-119396600	Active TSS	Fetal Intestine Large	intestine
25	chr3:119395000-119396600	Active TSS	HSMM	muscle
26	chr3:119395000-119396800	Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:119395000-119396800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:119395000-119396800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:119395000-119396800	Active TSS	Fetal Thymus	thymus
30	chr3:119395000-119397000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr3:119395000-119397000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:119395000-119397000	Active TSS	Stomach Smooth Muscle	stomach
33	chr3:119395200-119395800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr3:119395200-119395800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr3:119395200-119395800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr3:119395200-119395800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:119395200-119395800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr3:119395200-119395800	Flanking Active TSS	HUVEC	blood vessel
39	chr3:119395200-119396400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:119395200-119396400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:119395200-119396600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr3:119395200-119396600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:119395200-119396600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:119395200-119396600	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr3:119395200-119396600	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:119395200-119396600	Active TSS	Brain Germinal Matrix	brain
47	chr3:119395200-119396600	Active TSS	Placenta	Placenta
48	chr3:119395200-119396800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:119395200-119396800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:119395200-119396800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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