Variant report

Variant	rs9821916
Chromosome Location	chr3:52273787-52273788
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	CHD1	chr3:52272945-52273810	GM12878	blood:	n/a	chr3:52273186-52273196
2	POLR2A	chr3:52272259-52275014	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:52272974-52275139	PBDE	blood:	n/a	n/a
4	MTA3	chr3:52272162-52275133	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:52272416-52275284	PFSK-1	brain:	n/a	n/a
6	YY1	chr3:52273182-52273834	ECC-1	luminal epithelium:	n/a	chr3:52273188-52273197
7	POLR2A	chr3:52271840-52275220	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52272512-52273827	H1-neurons	neurons:	n/a	n/a
9	MYC	chr3:52271575-52273799	K562	blood:	n/a	chr3:52271704-52271713 chr3:52272927-52272937 chr3:52272941-52272951 chr3:52272692-52272702
10	YY1	chr3:52273247-52273862	H1-hESC	embryonic stem cell:	n/a	n/a
11	BCLAF1	chr3:52272918-52273816	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:52272486-52273821	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:52272555-52273844	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:52272102-52273788	K562	blood:	n/a	n/a
15	EGR1	chr3:52272984-52273848	HCT-116	colon:	n/a	chr3:52273189-52273202 chr3:52272985-52272995 chr3:52273187-52273197 chr3:52273233-52273242 chr3:52273232-52273241
16	CTCF	chr3:52273485-52273789	IMR90	lung:	n/a	chr3:52273641-52273649
17	YY1	chr3:52272912-52273854	GM12892	blood:	n/a	chr3:52273175-52273189 chr3:52273188-52273197
18	CTCF	chr3:52273457-52273834	Spleen_OC	spleen:	n/a	chr3:52273641-52273649
19	ZBTB7A	chr3:52272566-52273832	ECC-1	luminal epithelium:	n/a	chr3:52273517-52273528
20	MAX	chr3:52272949-52273821	SK-N-SH	brain:	n/a	n/a
21	MAX	chr3:52272026-52273832	HepG2	liver:	n/a	chr3:52272927-52272937 chr3:52272941-52272951 chr3:52272692-52272702
22	CTCF	chr3:52273280-52274011	A549	lung:	n/a	chr3:52273641-52273649
23	POLR2A	chr3:52272314-52273852	HL-60	blood:	n/a	n/a
24	YY1	chr3:52273397-52273826	GM12878	blood:	n/a	n/a
25	CTCF	chr3:52273411-52273812	GM12878	blood:	n/a	chr3:52273641-52273649
26	MAX	chr3:52271670-52273809	HepG2	liver:	n/a	chr3:52271704-52271713 chr3:52272927-52272937 chr3:52272941-52272951 chr3:52272692-52272702
27	POLR2A	chr3:52272514-52273844	GM12892	blood:	n/a	n/a
28	REST	chr3:52272191-52273896	H1-neurons	neurons:	n/a	chr3:52272233-52272243
29	POLR2A	chr3:52272765-52275094	H1-hESC	embryonic stem cell:	n/a	n/a
30	SMC3	chr3:52273129-52273800	Hela-S3	cervix:	n/a	chr3:52273173-52273183
31	MTA3	chr3:52273224-52273811	GM12878	blood:	n/a	n/a
32	ZBTB7A	chr3:52272622-52273791	ECC-1	luminal epithelium:	n/a	chr3:52273517-52273528
33	POLR2A	chr3:52272266-52273925	HL-60	blood:	n/a	n/a
34	ZNF384	chr3:52273556-52273836	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:52272326-52273798	GM12892	blood:	n/a	n/a
36	MXI1	chr3:52271350-52273925	IMR90	lung:	n/a	n/a
37	YY1	chr3:52272951-52273803	GM12891	blood:	n/a	chr3:52273175-52273189 chr3:52273188-52273197
38	YY1	chr3:52273313-52273815	SK-N-SH_RA	brain:	n/a	n/a
39	EBF1	chr3:52273547-52273795	GM12878	blood:	n/a	n/a
40	PML	chr3:52272190-52273965	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:52272395-52274484	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr3:52272591-52273790	HCT-116	colon:	n/a	n/a
43	POLR2A	chr3:52272461-52274957	GM12878	blood:	n/a	n/a
44	MAZ	chr3:52270816-52273788	IMR90	lung:	n/a	chr3:52271704-52271713 chr3:52272927-52272937 chr3:52272941-52272951
45	MAX	chr3:52272335-52273793	NB4	blood:	n/a	chr3:52272927-52272937 chr3:52272941-52272951 chr3:52272692-52272702
46	POLR2A	chr3:52272241-52274952	PFSK-1	brain:	n/a	n/a
47	MAX	chr3:52272945-52273807	K562	blood:	n/a	n/a
48	YY1	chr3:52272933-52273797	GM12878	blood:	n/a	chr3:52273175-52273189 chr3:52273188-52273197
49	POLR2A	chr3:52272546-52273849	SK-N-MC	brain:	n/a	n/a
50	MAX	chr3:52272479-52273799	ECC-1	luminal epithelium:	n/a	chr3:52272927-52272937 chr3:52272941-52272951 chr3:52272692-52272702

No.	Distal block	Cell Line	Cell type
1	chr3:52272619..52275147-chr3:52443057..52446254,5	K562	blood:
2	chr3:52272390..52274822-chr3:52406008..52407949,2	K562	blood:
3	chr3:52259472..52263342-chr3:52269626..52274061,4	MCF-7	breast:
4	chr3:52006492..52009228-chr3:52273747..52276252,2	K562	blood:
5	chr3:52271022..52275105-chr3:52320320..52325575,6	K562	blood:
6	chr3:52271015..52274727-chr3:52321912..52324165,4	K562	blood:
7	chr3:52271478..52274801-chr3:52443057..52446273,4	K562	blood:
8	chr3:52270811..52274971-chr3:52310538..52315239,11	K562	blood:
9	chr3:52262375..52268246-chr3:52270366..52274345,8	K562	blood:
10	chr3:52270811..52276588-chr3:52310648..52314131,11	K562	blood:
11	chr3:52273329..52274998-chr3:52327132..52329957,2	MCF-7	breast:
12	chr3:52027463..52030131-chr3:52273399..52277503,3	K562	blood:
13	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
14	chr3:52273385..52273886-chr3:133378506..133379006,2	NB4	blood:
15	chr3:52269470..52276026-chr3:52310334..52314212,10	MCF-7	breast:
16	chr3:52272807..52274330-chr3:52300733..52302349,2	MCF-7	breast:
17	chr3:52269533..52276077-chr3:52310385..52313504,11	MCF-7	breast:
18	chr3:52272181..52276088-chr3:52318615..52323958,11	MCF-7	breast:

Variant related genes	Relation type
TLR9	TF binding region
TWF2	TF binding region
ENSG00000239732	Chromatin interaction
ENSG00000207926	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000239557	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000173366	Chromatin interaction
ENSG00000272762	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10440116	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13318570	1.00[AMR][1000 genomes]
rs17052143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28413740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5743834	1.00[EUR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813489	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9813653	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9815559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828488	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834363	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836166	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842960	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9843055	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844178	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9868332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS 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	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52271800-52274200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:52272000-52273800	Active TSS	Aorta	Aorta
3	chr3:52272200-52273800	Active TSS	Ovary	ovary
4	chr3:52272200-52274000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:52272200-52274200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52272400-52273800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:52272400-52273800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:52272400-52274000	Active TSS	NHDF-Ad	bronchial
9	chr3:52272400-52274000	Active TSS	NHLF	lung
10	chr3:52272400-52274200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:52272600-52273800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:52272600-52273800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:52272600-52273800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:52272600-52273800	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr3:52272600-52273800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52272600-52273800	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr3:52272600-52273800	Active TSS	Lung	lung
18	chr3:52272600-52273800	Active TSS	Placenta Amnion	Placenta Amnion
19	chr3:52272600-52273800	Active TSS	Psoas Muscle	Psoas
20	chr3:52272600-52273800	Active TSS	Small Intestine	intestine
21	chr3:52272600-52273800	Active TSS	Thymus	Thymus
22	chr3:52272600-52274000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:52272600-52274000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:52272600-52274000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:52272600-52274000	Active TSS	GM12878-XiMat	blood
26	chr3:52272600-52274000	Active TSS	HSMM	muscle
27	chr3:52272600-52274000	Active TSS	NHEK	skin
28	chr3:52272600-52274200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:52272600-52274200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:52272600-52274200	Active TSS	A549	lung
31	chr3:52272600-52274400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:52272800-52273800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:52272800-52273800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:52272800-52273800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52272800-52273800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:52272800-52273800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:52272800-52273800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:52272800-52273800	Active TSS	Primary T cells from cord blood	blood
39	chr3:52272800-52273800	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr3:52272800-52273800	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:52272800-52273800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr3:52272800-52273800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:52272800-52273800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:52272800-52273800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52272800-52273800	Active TSS	Colon Smooth Muscle	Colon
46	chr3:52272800-52273800	Active TSS	Fetal Heart	heart
47	chr3:52272800-52273800	Active TSS	Fetal Stomach	stomach
48	chr3:52272800-52273800	Active TSS	Gastric	stomach
49	chr3:52272800-52273800	Active TSS	Pancreas	Pancrea
50	chr3:52272800-52273800	Active TSS	Rectal Mucosa Donor 31	rectum

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