Variant report

Variant	rs190910
Chromosome Location	chr3:139259726-139259727
allele	A/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	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	ATF2	chr3:139259459-139259825	GM12878	blood:	n/a	n/a
3	JUN	chr3:139259589-139259734	HepG2	liver:	n/a	n/a
4	GATA3	chr3:139259388-139259805	SH-SY5Y	brain:	n/a	chr3:139259774-139259783
5	NFIC	chr3:139259397-139259812	GM12878	blood:	n/a	n/a
6	FOXP2	chr3:139259719-139259954	SK-N-MC	brain:	n/a	n/a
7	KAP1	chr3:139259464-139260440	U2OS	brain:	n/a	n/a
8	GATA2	chr3:139259623-139259966	SH-SY5Y	brain:	n/a	chr3:139259774-139259783
9	RUNX3	chr3:139259510-139259808	GM12878	blood:	n/a	n/a
10	JUND	chr3:139259537-139259780	HepG2	liver:	n/a	n/a
11	EBF1	chr3:139259570-139259997	GM12878	blood:	n/a	chr3:139259806-139259817 chr3:139259807-139259817 chr3:139259820-139259831
12	EP300	chr3:139259590-139259947	SK-N-SH_RA	brain:	n/a	n/a
13	POLR2A	chr3:139259528-139259969	SK-N-MC	brain:	n/a	n/a
14	GTF2F1	chr3:139259717-139259869	H1-hESC	embryonic stem cell:	n/a	n/a
15	EP300	chr3:139259558-139259800	GM12878	blood:	n/a	n/a
16	RUNX3	chr3:139259416-139259921	GM12878	blood:	n/a	n/a
17	KAP1	chr3:139259465-139260908	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139251954..139254660-chr3:139259598..139262357,2	MCF-7	breast:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10935331	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs167188	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176990	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211586	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295501	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4564921	0.82[EUR][1000 genomes]
rs6797111	0.96[EUR][1000 genomes]
rs893704	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs9816597	0.96[EUR][1000 genomes]
rs9825927	0.94[EUR][1000 genomes]
rs9826668	0.93[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139257600-139259800	Active TSS	Ovary	ovary
2	chr3:139257800-139259800	Active TSS	Pancreas	Pancrea
3	chr3:139257800-139259800	Active TSS	HSMMtube	muscle
4	chr3:139258200-139259800	Active TSS	Fetal Brain Female	brain
5	chr3:139258600-139259800	Weak transcription	Spleen	Spleen
6	chr3:139258800-139260000	Active TSS	Fetal Muscle Trunk	muscle
7	chr3:139258800-139260000	Weak transcription	Lung	lung
8	chr3:139258800-139260200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr3:139259000-139259800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:139259000-139259800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr3:139259000-139259800	Weak transcription	Right Ventricle	heart
12	chr3:139259000-139260000	Enhancers	HMEC	breast
13	chr3:139259000-139260200	Enhancers	Placenta	Placenta
14	chr3:139259000-139260400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:139259200-139259800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:139259200-139259800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
17	chr3:139259200-139259800	Weak transcription	Esophagus	oesophagus
18	chr3:139259200-139259800	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr3:139259200-139260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:139259200-139260000	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr3:139259200-139260200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:139259200-139260200	Flanking Active TSS	Fetal Kidney	kidney
23	chr3:139259200-139260200	Flanking Active TSS	Fetal Lung	lung
24	chr3:139259200-139260400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:139259200-139260800	Enhancers	Brain Angular Gyrus	brain
26	chr3:139259200-139261000	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:139259200-139307000	Weak transcription	Aorta	Aorta
28	chr3:139259400-139259800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:139259400-139259800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
30	chr3:139259400-139259800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr3:139259400-139259800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
32	chr3:139259400-139259800	Enhancers	Brain Substantia Nigra	brain
33	chr3:139259400-139259800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr3:139259400-139259800	Flanking Active TSS	Fetal Brain Male	brain
35	chr3:139259400-139259800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr3:139259400-139259800	Bivalent Enhancer	HepG2	liver
37	chr3:139259400-139260000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
38	chr3:139259400-139260000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
39	chr3:139259400-139260000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr3:139259400-139260000	Enhancers	Rectal Smooth Muscle	rectum
41	chr3:139259400-139260200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:139259400-139260200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:139259400-139260200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:139259400-139260200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:139259400-139260600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:139259400-139260800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr3:139259400-139261200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:139259600-139259800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:139259600-139259800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
50	chr3:139259600-139259800	Enhancers	Brain Anterior Caudate	brain

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