Variant report

Variant	rs67683909
Chromosome Location	chr3:119362318-119362319
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	MAX	chr3:119361960-119362350	NB4	blood:	n/a	chr3:119362141-119362151 chr3:119362174-119362184
2	JUND	chr3:119361808-119362527	K562	blood:	n/a	chr3:119361827-119361835 chr3:119361827-119361835 chr3:119361827-119361834
3	TCF12	chr3:119361739-119362984	SK-N-SH	brain:	n/a	chr3:119361863-119361873
4	MYC	chr3:119361971-119362587	K562	blood:	n/a	chr3:119362141-119362151 chr3:119362174-119362184
5	PBX3	chr3:119362291-119362866	SK-N-SH	brain:	n/a	n/a
6	SP1	chr3:119362242-119362915	HCT-116	colon:	n/a	n/a
7	FOSL2	chr3:119362269-119362995	SK-N-SH	brain:	n/a	n/a
8	JUND	chr3:119362279-119362930	SK-N-SH	brain:	n/a	n/a
9	JUND	chr3:119362193-119362998	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr3:119362205-119362969	SK-N-SH	brain:	n/a	n/a
11	MAX	chr3:119361996-119362339	H1-hESC	embryonic stem cell:	n/a	chr3:119362141-119362151 chr3:119362174-119362184
12	E2F6	chr3:119362030-119362347	H1-hESC	embryonic stem cell:	n/a	n/a
13	RCOR1	chr3:119361907-119362327	K562	blood:	n/a	n/a
14	MAX	chr3:119361940-119362384	H1-hESC	embryonic stem cell:	n/a	chr3:119362141-119362151 chr3:119362174-119362184
15	FOSL1	chr3:119362266-119362969	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119361516..119364108-chr3:119364269..119367239,2	K562	blood:

Variant related genes	Relation type
POPDC2	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11914676	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923223	0.87[ASN][1000 genomes]
rs12487499	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488460	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12490779	0.93[ASN][1000 genomes]
rs12492456	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403631	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525836	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830115	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.87[ASN][1000 genomes]
rs17203235	0.93[ASN][1000 genomes]
rs1797827	0.97[ASN][1000 genomes]
rs1872432	0.93[ASN][1000 genomes]
rs1985121	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280578	0.87[ASN][1000 genomes]
rs2670292	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688629	0.97[ASN][1000 genomes]
rs2688630	0.97[ASN][1000 genomes]
rs2688631	0.97[ASN][1000 genomes]
rs2688634	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692616	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698283	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34097211	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34787881	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35256565	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688021	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688024	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524043	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525916	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540420	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572119	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575833	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579196	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783324	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789941	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790938	0.86[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6803814	0.87[ASN][1000 genomes]
rs68150601	0.87[ASN][1000 genomes]
rs71325388	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71325389	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613825	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8422	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876919	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119341400-119364600	Weak transcription	Liver	Liver
2	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
4	chr3:119352600-119367000	Weak transcription	Ovary	ovary
5	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:119356800-119364800	Weak transcription	Stomach Mucosa	stomach
8	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
12	chr3:119357800-119366600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:119357800-119367000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
18	chr3:119358200-119362800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:119358200-119366200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:119358200-119372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:119358400-119366800	Weak transcription	Esophagus	oesophagus
22	chr3:119358400-119367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:119358600-119365200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:119358600-119366600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:119358600-119371600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:119358600-119372400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:119358800-119362600	Genic enhancers	Fetal Heart	heart
30	chr3:119359800-119363600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr3:119360200-119362400	Strong transcription	Psoas Muscle	Psoas
32	chr3:119360200-119363000	Strong transcription	Primary T cells from cord blood	blood
33	chr3:119360400-119366600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:119360600-119363800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:119360600-119365400	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:119360800-119367800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:119361000-119362600	Enhancers	Right Atrium	heart
38	chr3:119361000-119362800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:119361000-119363200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:119361000-119363600	Weak transcription	Fetal Brain Male	brain
41	chr3:119361000-119363600	Enhancers	NHDF-Ad	bronchial
42	chr3:119361000-119363800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:119361000-119363800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:119361200-119363000	Enhancers	NHLF	lung
45	chr3:119361200-119363600	Enhancers	HSMM	muscle
46	chr3:119361200-119365800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:119361200-119366800	Weak transcription	Pancreas	Pancrea
48	chr3:119361200-119367000	Weak transcription	Gastric	stomach
49	chr3:119361200-119369000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus

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