Variant report

Variant	rs2273592
Chromosome Location	chr14:39645458-39645459
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	chr14:39643132-39645483	GM12892	blood:	n/a	n/a
2	POLR2A	chr14:39643640-39645498	GM12892	blood:	n/a	n/a
3	CHD1	chr14:39643485-39645701	IMR90	lung:	n/a	chr14:39644663-39644673
4	CREB1	chr14:39643207-39645484	HepG2	liver:	n/a	n/a
5	MYBL2	chr14:39643054-39645503	HepG2	liver:	n/a	n/a
6	POLR2A	chr14:39642960-39651251	H1-hESC	embryonic stem cell:	n/a	n/a
7	NFIC	chr14:39643501-39645806	HepG2	liver:	n/a	n/a
8	POLR2A	chr14:39643065-39645495	SK-N-MC	brain:	n/a	n/a
9	MYC	chr14:39643761-39645604	MCF10A-Er-Src	breast:	n/a	chr14:39644996-39645003
10	HEY1	chr14:39643699-39645520	HepG2	liver:	n/a	chr14:39644415-39644430
11	ARID3A	chr14:39643431-39645626	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:39643051-39648902	HepG2	liver:	n/a	n/a
13	CHD1	chr14:39643798-39646129	H1-hESC	embryonic stem cell:	n/a	chr14:39644663-39644673
14	POLR2A	chr14:39643266-39645854	GM12878	blood:	n/a	n/a
15	CREB1	chr14:39643869-39645539	HepG2	liver:	n/a	n/a
16	STAT3	chr14:39645448-39645549	MCF10A-Er-Src	breast:	n/a	n/a
17	HEY1	chr14:39643033-39645514	HepG2	liver:	n/a	chr14:39644415-39644430
18	POLR2A	chr14:39643164-39645482	GM12878	blood:	n/a	n/a
19	POLR2A	chr14:39643789-39645497	GM12891	blood:	n/a	n/a
20	POLR2A	chr14:39643219-39645602	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr14:39643466-39645589	HepG2	liver:	n/a	n/a
22	POLR2A	chr14:39643252-39645500	GM19099	blood:	n/a	n/a
23	SIN3A	chr14:39643894-39645463	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr14:39643261-39648811	K562	blood:	n/a	n/a
25	SREBP1	chr14:39643578-39645901	GM12878	blood:	n/a	n/a
26	NFIC	chr14:39643219-39645473	HepG2	liver:	n/a	n/a
27	MAX	chr14:39643153-39645546	HepG2	liver:	n/a	chr14:39644996-39645003
28	MBD4	chr14:39643296-39645794	HepG2	liver:	n/a	n/a
29	GATA1	chr14:39642268-39645466	PBDE	blood:	n/a	chr14:39644071-39644079
30	MBD4	chr14:39643120-39646667	HepG2	liver:	n/a	n/a
31	MYBL2	chr14:39643271-39645673	HepG2	liver:	n/a	n/a
32	POLR2A	chr14:39645403-39645598	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr14:39643181-39645467	HepG2	liver:	n/a	n/a
34	TEAD4	chr14:39643084-39646101	HepG2	liver:	n/a	n/a
35	SIN3AK20	chr14:39643749-39645536	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:39643730..39648156-chr14:39734640..39738499,10	MCF-7	breast:
2	chr14:39642546..39647225-chr14:39733415..39737853,13	MCF-7	breast:
3	chr14:39643409..39646477-chr14:39682252..39685201,4	MCF-7	breast:
4	chr14:39582116..39585012-chr14:39643452..39645860,4	MCF-7	breast:
5	chr14:39644686..39646338-chr14:39899658..39902040,2	K562	blood:

Variant related genes	Relation type
PNN	TF binding region
ENSG00000259083	TF binding region
ENSG00000258940	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000165355	Chromatin interaction
ENSG00000270503	Chromatin interaction
ENSG00000092208	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1002193	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129762	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10131369	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10134166	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10134656	0.82[AMR][1000 genomes]
rs10135561	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136637	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10140763	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10141081	0.82[AMR][1000 genomes]
rs10141924	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142117	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10142350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145476	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10146176	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10148712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040680	0.83[AMR][1000 genomes]
rs1050136	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11622731	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11622968	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623907	0.82[AMR][1000 genomes]
rs11623945	0.82[AMR][1000 genomes]
rs11624584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11626002	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627264	0.82[AMR][1000 genomes]
rs11628564	0.82[AMR][1000 genomes]
rs11628784	0.80[CEU][hapmap];0.84[ASN][1000 genomes]
rs11848067	0.82[AMR][1000 genomes]
rs11849209	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11851680	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587208	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13021	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379129	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17092044	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17092050	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17108696	0.82[AMR][1000 genomes]
rs17108948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144528	0.82[AMR][1000 genomes]
rs2277458	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs28414518	0.82[AMR][1000 genomes]
rs28437577	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28470602	0.82[AMR][1000 genomes]
rs28501673	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583114	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28666016	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28701960	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28821293	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs45622837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55737943	0.82[AMR][1000 genomes]
rs56064304	0.82[AMR][1000 genomes]
rs56105133	0.82[AMR][1000 genomes]
rs57326310	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57482489	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57555422	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58601678	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59465524	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7144625	0.82[AMR][1000 genomes]
rs7155307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7156264	0.83[YRI][hapmap]
rs74048710	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74048711	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs761805	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018720	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs926970	0.82[AMR][1000 genomes]
rs926971	0.82[JPT][hapmap]
rs993675	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS 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 miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2273592	SS18	cis	Temporal Cortex	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39643200-39645600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:39643200-39645600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr14:39643400-39645600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:39643400-39645600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr14:39643400-39645600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:39643400-39645600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:39643400-39645600	Active TSS	Fetal Intestine Small	intestine
8	chr14:39643400-39645600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr14:39643400-39645800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr14:39643600-39645600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:39643600-39645600	Active TSS	HSMMtube	muscle
12	chr14:39643600-39645600	Active TSS	NHDF-Ad	bronchial
13	chr14:39643600-39645600	Active TSS	NHLF	lung
14	chr14:39643600-39645800	Active TSS	Fetal Brain Female	brain
15	chr14:39643600-39645800	Active TSS	Psoas Muscle	Psoas
16	chr14:39643600-39645800	Active TSS	Right Ventricle	heart
17	chr14:39643600-39645800	Active TSS	K562	blood
18	chr14:39643600-39646000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr14:39643600-39646000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr14:39643800-39645600	Active TSS	Liver	Liver
21	chr14:39643800-39645600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr14:39643800-39645600	Active TSS	Fetal Intestine Large	intestine
23	chr14:39643800-39645800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:39643800-39646000	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr14:39643800-39646200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr14:39643800-39646600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr14:39644000-39645600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr14:39644000-39645600	Active TSS	Fetal Muscle Trunk	muscle
29	chr14:39644400-39645600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr14:39644400-39646200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
31	chr14:39644400-39646200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
32	chr14:39644600-39645800	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr14:39644800-39645600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr14:39644800-39645600	Transcr. at gene 5' and 3'	Fetal Lung	lung
35	chr14:39644800-39645800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr14:39644800-39645800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr14:39644800-39645800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr14:39644800-39645800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:39644800-39646400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr14:39644800-39646600	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr14:39645000-39645600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr14:39645000-39645600	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr14:39645000-39645800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr14:39645000-39645800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr14:39645000-39645800	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr14:39645000-39645800	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr14:39645000-39645800	Active TSS	Right Atrium	heart
48	chr14:39645000-39645800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr14:39645000-39646400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
50	chr14:39645000-39646400	Transcr. at gene 5' and 3'	A549	lung

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