Variant report

Variant	rs2302775
Chromosome Location	chr17:38182844-38182845
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	FOS	chr17:38182658-38182954	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr17:38182229-38182916	MCF-7	breast:	n/a	n/a
3	E2F4	chr17:38182725-38183575	MCF10A-Er-Src	breast:	n/a	n/a
4	NR2F2	chr17:38182298-38182929	MCF-7	breast:	n/a	n/a
5	CTCF	chr17:38182826-38184090	SK-N-SH	brain:	n/a	chr17:38183442-38183458 chr17:38183907-38183925 chr17:38183448-38183455 chr17:38183443-38183456 chr17:38183436-38183457 chr17:38183441-38183459 chr17:38183902-38183923
6	STAT3	chr17:38182220-38182911	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
7	STAT3	chr17:38182220-38182908	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
8	YY1	chr17:38182701-38183293	H1-hESC	embryonic stem cell:	n/a	chr17:38182950-38182962
9	YY1	chr17:38182835-38183068	K562	blood:	n/a	chr17:38182950-38182962
10	STAT3	chr17:38182465-38182990	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
11	FOS	chr17:38182080-38182982	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:38182813-38183515	HL-60	blood:	n/a	n/a
13	STAT3	chr17:38182660-38182942	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
14	MYC	chr17:38182411-38182944	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr17:38182800-38182950	AG04450	lung:	n/a	n/a
16	FOS	chr17:38182684-38182949	MCF10A-Er-Src	breast:	n/a	n/a
17	YY1	chr17:38182789-38183149	H1-hESC	embryonic stem cell:	n/a	chr17:38182950-38182962
18	POLR2A	chr17:38182792-38183860	K562	blood:	n/a	n/a
19	MYC	chr17:38182218-38182970	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr17:38182218-38183006	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr17:38182613-38182891	MCF10A-Er-Src	breast:	n/a	chr17:38182767-38182775
22	CTCF	chr17:38182840-38182990	GM12866	blood:	n/a	n/a
23	E2F6	chr17:38182772-38183730	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38170232..38173097-chr17:38181812..38184113,4	MCF-7	breast:
2	chr17:38170609..38173071-chr17:38181273..38184131,2	MCF-7	breast:
3	chr17:38181477..38183501-chr17:38217583..38219827,2	MCF-7	breast:
4	chr17:38178740..38181888-chr17:38181920..38184770,3	K562	blood:
5	chr17:38177803..38180808-chr17:38181920..38184987,3	K562	blood:
6	chr17:38181641..38185122-chr17:38333882..38336606,4	MCF-7	breast:
7	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:

Variant related genes	Relation type
MED24	TF binding region
ENSG00000108342	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000126351	Chromatin interaction
ENSG00000265799	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1042657	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10852937	0.92[CHD][hapmap]
rs2071369	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2071370	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2227324	0.94[ASN][1000 genomes]
rs2227338	0.94[ASN][1000 genomes]
rs2302778	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826330	0.86[CHB][hapmap]
rs3859190	0.86[CHB][hapmap]
rs3934886	0.81[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4795411	0.86[CHB][hapmap]
rs6503532	0.94[ASN][1000 genomes]
rs6503534	0.81[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs709592	0.81[YRI][hapmap]
rs7503939	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070452	0.83[ASN][1000 genomes]
rs921651	0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap]
rs9899955	0.95[ASN][1000 genomes]
rs9913632	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2302775	KRTAP4-2	cis	parietal	SCAN
rs2302775	MED24	cis	Muscle Skeletal	GTEx
rs2302775	MED24	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
2	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
7	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr17:38175000-38193800	Strong transcription	HepG2	liver
14	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
15	chr17:38175200-38193200	Strong transcription	Dnd41	blood
16	chr17:38175400-38188200	Weak transcription	Fetal Heart	heart
17	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
18	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:38175800-38183400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
23	chr17:38176000-38189800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
26	chr17:38176200-38183400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr17:38176200-38183400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:38176200-38193800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr17:38176400-38192400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr17:38176600-38183000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:38177400-38184000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:38177600-38183200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr17:38177800-38183000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:38177800-38185400	Strong transcription	GM12878-XiMat	blood
35	chr17:38177800-38191000	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr17:38178000-38187800	Strong transcription	Right Ventricle	heart
37	chr17:38178200-38183200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr17:38178200-38192600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:38178400-38183200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr17:38178600-38183000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:38178600-38191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:38178800-38184600	Weak transcription	HSMMtube	muscle
43	chr17:38179000-38184000	Genic enhancers	Muscle Satellite Cultured Cells	--
44	chr17:38179000-38192600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr17:38179200-38183200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:38179800-38183000	Strong transcription	Adipose Nuclei	Adipose
47	chr17:38180400-38183200	Strong transcription	Fetal Intestine Small	intestine
48	chr17:38180400-38183400	Enhancers	HUVEC	blood vessel
49	chr17:38180400-38183800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr17:38180400-38191200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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