Variant report

Variant	rs28384824
Chromosome Location	chr1:171221720-171221721
allele	C/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	RUNX3	chr1:171221690-171222012	GM12878	blood:	n/a	n/a
2	ATF2	chr1:171221699-171222048	GM12878	blood:	n/a	n/a
3	BHLHE40	chr1:171221707-171222078	GM12878	blood:	n/a	n/a
4	TCF3	chr1:171221557-171222069	GM12878	blood:	n/a	chr1:171221820-171221833 chr1:171221840-171221856
5	TCF12	chr1:171221663-171222025	GM12878	blood:	n/a	n/a
6	TCF3	chr1:171221520-171222086	GM12878	blood:	n/a	chr1:171221820-171221833 chr1:171221840-171221856
7	EP300	chr1:171221694-171222057	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:171221630-171222017	GM12892	blood:	n/a	n/a
9	RUNX3	chr1:171221656-171222054	GM12878	blood:	n/a	n/a
10	ZEB1	chr1:171221647-171222053	GM12878	blood:	n/a	chr1:171221842-171221853
11	CTCF	chr1:171221600-171221750	HCPEpiC	choroid plexus:	n/a	n/a
12	CTCF	chr1:171221600-171221750	AG04449	skin:	n/a	n/a
13	MAZ	chr1:171221712-171222044	GM12878	blood:	n/a	n/a
14	TCF12	chr1:171221616-171222023	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171219827..171222241-chr1:171222983..171225833,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231424	TF binding region
ENSG00000206692	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs28369797	0.94[AFR][1000 genomes]
rs28369800	0.83[AFR][1000 genomes]
rs28369869	0.94[AFR][1000 genomes]
rs28369880	0.94[AFR][1000 genomes]
rs28369899	0.94[AFR][1000 genomes]
rs28369907	0.88[AFR][1000 genomes]
rs28369908	0.94[AFR][1000 genomes]
rs28369911	0.94[AFR][1000 genomes]
rs61098520	0.94[AFR][1000 genomes]
rs74122248	0.94[AFR][1000 genomes]
rs74122253	0.94[AFR][1000 genomes]
rs74122288	0.94[AFR][1000 genomes]
rs74122291	0.94[AFR][1000 genomes]
rs74122299	1.00[AFR][1000 genomes]
rs74122301	1.00[AFR][1000 genomes]
rs74122302	1.00[AFR][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171220200-171221800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
2	chr1:171221000-171221800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr1:171221000-171221800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:171221000-171222000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:171221000-171222000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr1:171221000-171222000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:171221000-171222000	Bivalent Enhancer	Fetal Thymus	thymus
8	chr1:171221000-171222200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:171221000-171222200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr1:171221000-171222600	Enhancers	Dnd41	blood
11	chr1:171221000-171223800	Weak transcription	HMEC	breast
12	chr1:171221000-171224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:171221000-171226000	Weak transcription	Fetal Kidney	kidney
14	chr1:171221000-171226600	Weak transcription	Esophagus	oesophagus
15	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:171221200-171221800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:171221200-171221800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:171221200-171221800	Enhancers	Primary B cells from cord blood	blood
19	chr1:171221200-171221800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:171221200-171221800	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:171221200-171221800	Enhancers	Pancreas	Pancrea
22	chr1:171221200-171221800	Enhancers	NHEK	skin
23	chr1:171221200-171222000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:171221200-171222000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:171221200-171222000	Enhancers	Fetal Muscle Trunk	muscle
26	chr1:171221200-171222000	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr1:171221200-171222200	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:171221200-171223600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:171221200-171223600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:171221200-171223600	Weak transcription	Osteobl	bone
31	chr1:171221200-171223800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:171221200-171224400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:171221200-171224400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:171221200-171224600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:171221200-171226000	Weak transcription	Liver	Liver
36	chr1:171221200-171226000	Weak transcription	Fetal Lung	lung
37	chr1:171221200-171226400	Weak transcription	Right Atrium	heart
38	chr1:171221200-171227200	Enhancers	Fetal Intestine Small	intestine
39	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
40	chr1:171221400-171221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:171221400-171221800	Bivalent Enhancer	Fetal Stomach	stomach
42	chr1:171221400-171223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:171221400-171223800	Weak transcription	NH-A	brain
44	chr1:171221400-171226200	Weak transcription	Fetal Heart	heart
45	chr1:171221600-171221800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:171221600-171221800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
47	chr1:171221600-171221800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
48	chr1:171221600-171221800	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:171221600-171222000	Enhancers	Gastric	stomach
50	chr1:171221600-171222000	Enhancers	HSMMtube	muscle

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