Variant report

Variant	rs9870144
Chromosome Location	chr3:158390984-158390985
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	SIN3AK20	chr3:158389652-158391089	MCF-7	breast:	n/a	n/a
2	GATA1	chr3:158390191-158390986	PBDE	blood:	n/a	n/a
3	TCF12	chr3:158389862-158391023	A549	lung:	n/a	n/a
4	RCOR1	chr3:158390070-158391259	IMR90	lung:	n/a	n/a
5	POLR2A	chr3:158381091-158391011	PBDE	blood:	n/a	n/a
6	CTCF	chr3:158389528-158391125	A549	lung:	n/a	chr3:158390572-158390580 chr3:158390569-158390587 chr3:158390571-158390592
7	MXI1	chr3:158389379-158391135	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158361656..158363521-chr3:158390089..158391771,2	MCF-7	breast:
2	chr3:158377989..158381016-chr3:158389998..158392287,3	MCF-7	breast:
3	chr3:158374171..158375927-chr3:158390841..158393730,2	MCF-7	breast:
4	chr3:158362274..158363819-chr3:158388698..158391198,2	MCF-7	breast:

Variant related genes	Relation type
LXN	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12107056	0.94[AFR][1000 genomes]
rs12107594	1.00[MEX][hapmap]
rs12108046	0.98[AFR][1000 genomes]
rs13318929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13319134	0.98[AFR][1000 genomes]
rs13319269	0.98[AFR][1000 genomes]
rs13323588	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16829129	1.00[MKK][hapmap]
rs28657028	0.98[AFR][1000 genomes]
rs58105681	0.94[AFR][1000 genomes]
rs59718588	0.84[AFR][1000 genomes]
rs61348783	0.84[AFR][1000 genomes]
rs6768676	0.98[AFR][1000 genomes]
rs6793303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6803849	0.83[AFR][1000 genomes]
rs73024708	0.98[AFR][1000 genomes]
rs7632746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9290026	0.98[AFR][1000 genomes]
rs9812197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9813394	0.83[AFR][1000 genomes]
rs9848956	0.98[AFR][1000 genomes]
rs9872702	0.93[YRI][hapmap];0.98[AFR][1000 genomes]
rs9873296	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158364800-158391000	Strong transcription	Dnd41	blood
2	chr3:158386200-158407800	Weak transcription	HepG2	liver
3	chr3:158389200-158391200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:158389400-158391000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr3:158389400-158391000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:158389400-158396200	Weak transcription	K562	blood
7	chr3:158389600-158391000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr3:158389600-158391000	Flanking Active TSS	Fetal Thymus	thymus
9	chr3:158389800-158391000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:158389800-158391000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:158390000-158391000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:158390200-158391000	Active TSS	Pancreas	Pancrea
13	chr3:158390200-158392400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:158390200-158397600	Weak transcription	HSMMtube	muscle
15	chr3:158390200-158402800	Weak transcription	HSMM	muscle
16	chr3:158390400-158391000	Active TSS	Fetal Brain Male	brain
17	chr3:158390400-158401000	Weak transcription	NHDF-Ad	bronchial
18	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
19	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:158390600-158391000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr3:158390600-158391000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr3:158390600-158391000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr3:158390600-158391000	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr3:158390600-158391000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr3:158390600-158391000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr3:158390600-158391000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:158390600-158391000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr3:158390600-158391000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr3:158390600-158391000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr3:158390600-158391000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:158390600-158391000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:158390600-158391000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr3:158390600-158391000	Enhancers	Fetal Heart	heart
34	chr3:158390600-158391000	Flanking Active TSS	Fetal Kidney	kidney
35	chr3:158390600-158391000	Flanking Active TSS	Fetal Lung	lung
36	chr3:158390600-158391000	Enhancers	Placenta	Placenta
37	chr3:158390600-158391000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr3:158390600-158391000	Flanking Active TSS	Thymus	Thymus
39	chr3:158390600-158391000	Flanking Active TSS	A549	lung
40	chr3:158390600-158391000	Flanking Active TSS	GM12878-XiMat	blood
41	chr3:158390600-158391000	Flanking Active TSS	NHEK	skin
42	chr3:158390600-158391000	Flanking Active TSS	NHLF	lung
43	chr3:158390600-158391200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:158390600-158394800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:158390600-158394800	Weak transcription	Liver	Liver
46	chr3:158390600-158397400	Weak transcription	NH-A	brain
47	chr3:158390600-158410600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:158390800-158391000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:158390800-158391000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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