Variant report

Variant	rs1864830
Chromosome Location	chr2:38828538-38828539
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	POLR2A	chr2:38828488-38830465	H1-hESC	embryonic stem cell:	n/a	n/a
2	RCOR1	chr2:38828426-38831063	IMR90	lung:	n/a	n/a
3	SIN3AK20	chr2:38828533-38831144	MCF-7	breast:	n/a	n/a
4	TCF12	chr2:38828537-38831166	A549	lung:	n/a	n/a
5	RAD21	chr2:38827547-38831481	SK-N-SH	brain:	n/a	n/a
6	PML	chr2:38828044-38828928	K562	blood:	n/a	n/a
7	HEY1	chr2:38828474-38830907	HepG2	liver:	n/a	chr2:38829898-38829913 chr2:38830197-38830212
8	MXI1	chr2:38828504-38828695	K562	blood:	n/a	n/a
9	POLR2A	chr2:38828464-38828958	HepG2	liver:	n/a	n/a
10	GATA3	chr2:38828314-38828737	SH-SY5Y	brain:	n/a	n/a
11	MYC	chr2:38828505-38828550	MCF10A-Er-Src	breast:	n/a	n/a
12	REST	chr2:38828498-38831160	H1-neurons	neurons:	n/a	chr2:38830014-38830027 chr2:38829373-38829386 chr2:38830026-38830039 chr2:38829806-38829819
13	CEBPB	chr2:38828289-38829004	K562	blood:	n/a	n/a
14	EP300	chr2:38828217-38828721	GM12878	blood:	n/a	n/a
15	SIN3A	chr2:38828520-38831200	H1-hESC	embryonic stem cell:	n/a	chr2:38830115-38830126 chr2:38829851-38829864
16	CHD1	chr2:38827485-38831648	IMR90	lung:	n/a	n/a
17	SMC3	chr2:38827460-38831532	SK-N-SH	brain:	n/a	chr2:38830755-38830765 chr2:38830289-38830299
18	POLR2A	chr2:38828297-38829102	MCF10A-Er-Src	breast:	n/a	n/a
19	TEAD4	chr2:38828436-38829162	HepG2	liver:	n/a	chr2:38828789-38828798
20	POLR2A	chr2:38821640-38832164	K562	blood:	n/a	n/a
21	TEAD4	chr2:38828475-38829136	K562	blood:	n/a	chr2:38828789-38828798
22	TEAD4	chr2:38828383-38828929	K562	blood:	n/a	chr2:38828789-38828798
23	ZNF384	chr2:38827562-38828538	K562	blood:	n/a	chr2:38828250-38828258
24	HCFC1	chr2:38828046-38831217	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:38828372-38830880	HepG2	liver:	n/a	n/a
26	TEAD4	chr2:38828530-38828897	H1-hESC	embryonic stem cell:	n/a	chr2:38828789-38828798
27	IRF1	chr2:38827592-38829041	K562	blood:	n/a	chr2:38828237-38828244
28	STAT3	chr2:38828163-38828863	MCF10A-Er-Src	breast:	n/a	chr2:38828762-38828773
29	UBTF	chr2:38827334-38831119	K562	blood:	n/a	n/a
30	CEBPB	chr2:38828481-38829114	Hela-S3	cervix:	n/a	n/a
31	CHD1	chr2:38827968-38829446	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr2:38825282-38829280	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38827534..38829774-chr2:38906960..38909388,3	K562	blood:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
5	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
6	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
7	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
8	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
9	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
10	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235586	TF binding region
HNRNPLL	TF binding region
ENSG00000143891	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000232518	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10495880	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987111	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990659	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991911	0.94[EUR][1000 genomes]
rs12995222	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996029	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011896	0.96[AFR][1000 genomes]
rs1540436	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17421378	0.81[EUR][1000 genomes]
rs17421503	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17421545	0.85[ASN][1000 genomes]
rs17421587	0.82[EUR][1000 genomes]
rs17421743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493363	0.84[ASN][1000 genomes]
rs17493370	0.84[ASN][1000 genomes]
rs17493419	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17493538	0.83[ASN][1000 genomes]
rs17493573	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17493594	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17493839	0.84[ASN][1000 genomes]
rs17603796	0.80[ASN][1000 genomes]
rs1864828	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1864829	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213851	0.81[ASN][1000 genomes]
rs34462852	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34533895	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34688430	0.88[ASN][1000 genomes]
rs34821677	0.88[ASN][1000 genomes]
rs35151237	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35219064	0.95[EUR][1000 genomes]
rs35378647	0.88[ASN][1000 genomes]
rs35492507	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35581112	0.91[ASN][1000 genomes]
rs35679136	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35734673	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35869291	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4268910	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4536633	0.88[ASN][1000 genomes]
rs55948796	0.88[ASN][1000 genomes]
rs56208611	0.89[ASN][1000 genomes]
rs56217714	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6704829	0.89[ASN][1000 genomes]
rs6710118	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6722560	0.88[ASN][1000 genomes]
rs6731029	0.89[ASN][1000 genomes]
rs6733848	0.89[ASN][1000 genomes]
rs6745023	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6749343	0.94[EUR][1000 genomes]
rs6750764	0.88[ASN][1000 genomes]
rs67772386	0.82[EUR][1000 genomes]
rs68109027	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72905846	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72905865	0.95[ASN][1000 genomes]
rs72907903	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573095	0.80[ASN][1000 genomes]
rs934394	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs934395	0.83[AFR][1000 genomes];0.82[ASN][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active 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 miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38822400-38828600	Weak transcription	Lung	lung
2	chr2:38822800-38830400	Active TSS	Primary T cells fromperipheralblood	blood
3	chr2:38825000-38830600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:38825200-38831000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:38825600-38830800	Active TSS	Stomach Smooth Muscle	stomach
6	chr2:38825800-38828800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:38826200-38830800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:38826400-38830600	Active TSS	K562	blood
9	chr2:38826400-38831400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:38826800-38830600	Active TSS	NHLF	lung
11	chr2:38826800-38831000	Active TSS	Duodenum Mucosa	Duodenum
12	chr2:38827000-38828600	Active TSS	Brain Cingulate Gyrus	brain
13	chr2:38827000-38830600	Active TSS	Aorta	Aorta
14	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:38827000-38830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr2:38827000-38830800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:38827000-38831400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr2:38827200-38830400	Active TSS	HMEC	breast
20	chr2:38827200-38830600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:38827200-38830600	Active TSS	NH-A	brain
22	chr2:38827200-38830800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:38827200-38830800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr2:38827200-38830800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:38827200-38830800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:38827200-38830800	Active TSS	Fetal Intestine Small	intestine
27	chr2:38827200-38831000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:38827200-38831000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr2:38827200-38831000	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr2:38827200-38831200	Active TSS	Brain Germinal Matrix	brain
31	chr2:38827400-38828800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr2:38827400-38828800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr2:38827400-38828800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr2:38827400-38830600	Active TSS	Fetal Stomach	stomach
35	chr2:38827400-38830800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr2:38827400-38830800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr2:38827400-38830800	Bivalent/Poised TSS	HepG2	liver
38	chr2:38827400-38831000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr2:38827400-38831000	Active TSS	Right Ventricle	heart
40	chr2:38827400-38831200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:38827600-38828600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:38827600-38828600	Flanking Active TSS	Fetal Brain Female	brain
43	chr2:38827600-38829200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:38827600-38829200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:38827600-38830600	Active TSS	Colon Smooth Muscle	Colon
46	chr2:38827600-38830800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:38827600-38830800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr2:38827600-38830800	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr2:38827600-38830800	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr2:38827600-38830800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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