Variant report

Variant	rs73924016
Chromosome Location	chr2:39662481-39662482
allele	C/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	UBTF	chr2:39662309-39665492	K562	blood:	n/a	n/a
2	MXI1	chr2:39662210-39666175	SK-N-SH	brain:	n/a	n/a
3	JUND	chr2:39662346-39662615	K562	blood:	n/a	n/a
4	EP300	chr2:39662385-39662657	K562	blood:	n/a	n/a
5	GTF2F1	chr2:39662433-39662486	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr2:39662397-39662579	H1-hESC	embryonic stem cell:	n/a	n/a
7	RCOR1	chr2:39662197-39662671	K562	blood:	n/a	n/a
8	ZNF263	chr2:39662245-39665558	HEK293-T-REx	kidney:	n/a	chr2:39664436-39664445 chr2:39664470-39664479 chr2:39663909-39663918 chr2:39664443-39664464 chr2:39664471-39664492
9	GATA2	chr2:39662311-39662822	SH-SY5Y	brain:	n/a	n/a
10	GATA3	chr2:39662458-39662861	SH-SY5Y	brain:	n/a	n/a
11	SIN3A	chr2:39662438-39662716	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39661430..39663106-chr2:39773041..39775918,2	MCF-7	breast:
2	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
3	chr2:39662097..39664715-chr2:39993095..39995663,2	K562	blood:
4	chr2:39655304..39658022-chr2:39658367..39662517,3	K562	blood:
5	chr2:39661305..39663930-chr2:39740460..39742003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10490305	0.81[AFR][1000 genomes]
rs11886110	0.82[AFR][1000 genomes]
rs11886434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895366	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11898704	0.81[AFR][1000 genomes]
rs11902188	0.84[AFR][1000 genomes]
rs55750780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55961227	0.85[AFR][1000 genomes]
rs56928728	0.82[AFR][1000 genomes]
rs57084694	1.00[AFR][1000 genomes]
rs58824151	0.85[AFR][1000 genomes]
rs59896787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60394429	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544225	0.82[AFR][1000 genomes]
rs6712399	0.84[AFR][1000 genomes]
rs6723987	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6727395	0.84[AFR][1000 genomes]
rs6751506	0.84[AFR][1000 genomes]
rs73923887	0.85[AFR][1000 genomes]
rs73923888	0.85[AFR][1000 genomes]
rs73923889	0.85[AFR][1000 genomes]
rs73923895	0.81[AFR][1000 genomes]
rs73924011	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7565210	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591563	0.82[AFR][1000 genomes]
rs7599017	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39658600-39662800	Enhancers	Stomach Mucosa	stomach
2	chr2:39658600-39663000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr2:39659000-39663000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39659200-39662600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39659200-39663400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:39660000-39663200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:39660000-39663400	Flanking Active TSS	K562	blood
8	chr2:39660200-39663200	Enhancers	Small Intestine	intestine
9	chr2:39660400-39662600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:39660800-39662600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:39661000-39663000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:39661000-39666000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:39661200-39663000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:39661200-39663000	Flanking Active TSS	Fetal Heart	heart
15	chr2:39661200-39665000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:39661400-39662600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:39661400-39662600	Flanking Active TSS	Fetal Kidney	kidney
18	chr2:39661400-39663200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:39661400-39663200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:39661400-39663400	Flanking Active TSS	Fetal Brain Female	brain
21	chr2:39661400-39664000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:39661400-39665000	Active TSS	Right Atrium	heart
23	chr2:39661600-39662600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:39661600-39662600	Enhancers	Fetal Thymus	thymus
25	chr2:39661600-39662600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr2:39661600-39662600	Flanking Active TSS	HMEC	breast
27	chr2:39661600-39662800	Enhancers	Spleen	Spleen
28	chr2:39661600-39663200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr2:39661600-39663400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:39661600-39663400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr2:39661600-39663400	Flanking Active TSS	Hela-S3	cervix
32	chr2:39661600-39663600	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr2:39661600-39663800	Flanking Active TSS	Dnd41	blood
34	chr2:39661800-39662600	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr2:39661800-39663000	Flanking Active TSS	NHEK	skin
36	chr2:39661800-39663200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:39661800-39663200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:39661800-39663600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:39661800-39664000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:39661800-39665200	Active TSS	HSMMtube	muscle
41	chr2:39661800-39667000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:39661800-39667000	Active TSS	Aorta	Aorta
43	chr2:39662000-39663600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:39662000-39665000	Active TSS	Stomach Smooth Muscle	stomach
45	chr2:39662000-39665200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:39662000-39665200	Active TSS	NHLF	lung
47	chr2:39662000-39665400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:39662000-39665400	Active TSS	HSMM	muscle
49	chr2:39662000-39665600	Active TSS	Right Ventricle	heart
50	chr2:39662000-39665800	Active TSS	Pancreatic Islets	Pancreatic Islet

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