Variant report

Variant	rs4940110
Chromosome Location	chr18:45458519-45458520
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	POLR2A	chr18:45456413-45458569	NB4	blood:	n/a	n/a
2	RAD21	chr18:45458068-45458529	MCF-7	breast:	n/a	n/a
3	POLR2A	chr18:45454367-45459190	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr18:45455632-45459226	MCF10A-Er-Src	breast:	n/a	n/a
5	RAD21	chr18:45457309-45458677	SK-N-SH	brain:	n/a	n/a
6	SMC3	chr18:45458101-45458635	GM12878	blood:	n/a	n/a
7	EBF1	chr18:45458062-45458532	GM12878	blood:	n/a	n/a
8	RFX5	chr18:45457233-45458831	Hela-S3	cervix:	n/a	chr18:45457534-45457543 chr18:45458237-45458245 chr18:45457610-45457619
9	POLR2A	chr18:45454672-45458824	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr18:45457261-45458973	SK-N-MC	brain:	n/a	n/a
11	CUX1	chr18:45458465-45458652	GM12878	blood:	n/a	n/a
12	RAD21	chr18:45457572-45458564	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr18:45456195-45458632	HL-60	blood:	n/a	n/a
14	POLR2A	chr18:45456033-45458795	GM12891	blood:	n/a	n/a
15	RCOR1	chr18:45457169-45458590	GM12878	blood:	n/a	n/a
16	TBP	chr18:45457312-45458607	GM12878	blood:	n/a	n/a
17	POLR2A	chr18:45455468-45458915	K562	blood:	n/a	n/a
18	MAX	chr18:45456197-45458675	A549	lung:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
19	POLR2A	chr18:45456144-45458519	GM19099	blood:	n/a	n/a
20	MTA3	chr18:45457505-45458719	GM12878	blood:	n/a	n/a
21	POLR2A	chr18:45456087-45458693	HepG2	liver:	n/a	n/a
22	MAFK	chr18:45458027-45458722	K562	blood:	n/a	n/a
23	ELK1	chr18:45458440-45458756	GM12878	blood:	n/a	n/a
24	POLR2A	chr18:45456078-45458603	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr18:45458246-45458563	K562	blood:	n/a	n/a
26	MAZ	chr18:45456131-45458527	IMR90	lung:	n/a	chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
27	CTCF	chr18:45458075-45458714	K562	blood:	n/a	n/a
28	IRF1	chr18:45456684-45458589	K562	blood:	n/a	chr18:45457614-45457628 chr18:45456746-45456760 chr18:45458462-45458476 chr18:45457802-45457816
29	SPI1	chr18:45457913-45458739	HL-60	blood:	n/a	chr18:45458219-45458232 chr18:45458623-45458636 chr18:45458626-45458635 chr18:45458624-45458637
30	MXI1	chr18:45456060-45458741	IMR90	lung:	n/a	n/a
31	RUNX3	chr18:45457255-45458529	GM12878	blood:	n/a	chr18:45458341-45458350
32	HCFC1	chr18:45455600-45459758	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr18:45456056-45458954	GM12878	blood:	n/a	n/a
34	POLR2A	chr18:45456192-45458638	K562	blood:	n/a	n/a
35	MXI1	chr18:45455670-45458696	SK-N-SH	brain:	n/a	n/a
36	RELA	chr18:45457404-45458632	GM18505	blood:	n/a	n/a
37	MAX	chr18:45455869-45458539	Hela-S3	cervix:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
38	RELA	chr18:45457695-45458611	GM19099	blood:	n/a	n/a
39	POLR2A	chr18:45455888-45459386	Hela-S3	cervix:	n/a	n/a
40	MYC	chr18:45456240-45458537	NB4	blood:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
41	POLR2A	chr18:45457106-45458521	PBDE	blood:	n/a	n/a
42	POLR2A	chr18:45456198-45458710	HL-60	blood:	n/a	n/a
43	ARID3A	chr18:45457587-45458669	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:45448291..45450129-chr18:45457101..45459149,2	MCF-7	breast:
2	chr18:45422809..45427886-chr18:45455832..45459212,8	MCF-7	breast:
3	chr18:45458331..45460939-chr18:45561622..45564314,2	K562	blood:
4	chr18:45457936..45459581-chr18:45522909..45525211,2	K562	blood:
5	chr18:45457637..45459201-chr18:45523865..45526054,2	MCF-7	breast:
6	chr18:45457832..45458760-chr18:45548781..45549306,2	MCF-7	breast:
7	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10432199	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10502890	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10853560	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11082638	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11082639	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11082641	0.93[CEU][hapmap]
rs11874858	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12457664	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12458238	0.82[CEU][hapmap]
rs12604337	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12605333	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12956483	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12968107	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12968493	0.85[CEU][hapmap]
rs12969725	0.85[CEU][hapmap]
rs1539871	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1539872	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573362	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1573363	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613672	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1631576	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17741998	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1787176	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1787185	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs1787186	0.80[CEU][hapmap]
rs1787193	0.83[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787194	0.83[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787196	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787197	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1792653	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1792655	0.83[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1792668	0.85[CEU][hapmap]
rs1792669	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792670	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792671	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs1792672	0.81[EUR][1000 genomes]
rs1792674	0.81[CEU][hapmap]
rs1792675	0.83[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792679	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs1792681	0.81[JPT][hapmap]
rs1792682	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs1792683	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1792686	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs1792687	0.81[CEU][hapmap]
rs1981	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs2000708	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2000709	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2012555	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2096932	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2096933	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28548478	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35710478	0.81[AMR][1000 genomes]
rs3813068	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4939672	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4940102	0.82[CEU][hapmap]
rs4940109	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4940120	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4940127	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61513611	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62086544	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6507790	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6507791	0.86[CEU][hapmap]
rs7228393	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7231538	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7232764	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7232893	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7233129	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7236177	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7237544	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7243502	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs729112	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs747952	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs747953	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs765213	0.96[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8084915	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8095519	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8097580	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8097912	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097925	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8099127	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8099681	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs948600	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs948601	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs948602	0.82[CEU][hapmap]
rs948603	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs948604	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9946556	0.83[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9947494	0.87[EUR][1000 genomes]
rs9950207	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9955626	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9961652	0.84[ASN][1000 genomes]
rs9966637	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9966964	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3446751	chr18:45455904-45459152	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45454600-45458600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:45454600-45458600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr18:45454800-45458600	Active TSS	K562	blood
4	chr18:45455000-45458600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:45455000-45458600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr18:45455200-45458600	Active TSS	Fetal Kidney	kidney
7	chr18:45455800-45458600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr18:45456200-45458600	Active TSS	Brain Cingulate Gyrus	brain
9	chr18:45456800-45458600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr18:45457400-45458600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr18:45457400-45458600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr18:45457600-45458600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr18:45457600-45458600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr18:45457800-45458600	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr18:45457800-45458600	Flanking Active TSS	Fetal Thymus	thymus
16	chr18:45457800-45458600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr18:45457800-45458800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr18:45457800-45458800	Flanking Active TSS	Thymus	Thymus
19	chr18:45457800-45458800	Flanking Active TSS	Hela-S3	cervix
20	chr18:45457800-45458800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr18:45457800-45459000	Flanking Active TSS	Dnd41	blood
22	chr18:45458000-45458600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr18:45458000-45458600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr18:45458000-45458600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr18:45458000-45458600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr18:45458000-45458600	Flanking Active TSS	Fetal Brain Male	brain
27	chr18:45458000-45458600	Flanking Active TSS	A549	lung
28	chr18:45458000-45458600	Flanking Active TSS	HepG2	liver
29	chr18:45458000-45458600	Flanking Active TSS	NHEK	skin
30	chr18:45458000-45458800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr18:45458000-45458800	Enhancers	Fetal Heart	heart
32	chr18:45458000-45458800	Flanking Active TSS	Stomach Mucosa	stomach
33	chr18:45458200-45458600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
34	chr18:45458200-45458600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr18:45458200-45458600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr18:45458200-45458600	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr18:45458200-45458600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr18:45458200-45458600	Flanking Active TSS	GM12878-XiMat	blood
39	chr18:45458200-45458800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr18:45458200-45458800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr18:45458200-45458800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr18:45458200-45458800	Enhancers	Placenta	Placenta
43	chr18:45458200-45463400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:45458400-45458600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr18:45458400-45458600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr18:45458400-45458600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr18:45458400-45458600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr18:45458400-45458600	Enhancers	Liver	Liver
49	chr18:45458400-45458600	Enhancers	Brain Angular Gyrus	brain
50	chr18:45458400-45458600	Enhancers	Brain Anterior Caudate	brain

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