Variant report

Variant	rs11874858
Chromosome Location	chr18:45457818-45457819
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	EP300	chr18:45457267-45458008	GM12878	blood:	n/a	n/a
2	POLR2A	chr18:45456206-45458143	K562	blood:	n/a	n/a
3	USF1	chr18:45457585-45458115	ECC-1	luminal epithelium:	n/a	chr18:45457861-45457872
4	MAX	chr18:45457051-45458252	ECC-1	luminal epithelium:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
5	MAX	chr18:45457271-45458517	A549	lung:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
6	CCNT2	chr18:45456398-45458354	K562	blood:	n/a	chr18:45456627-45456636 chr18:45456508-45456517
7	POLR2A	chr18:45456413-45458569	NB4	blood:	n/a	n/a
8	POLR2A	chr18:45457287-45458130	U87	brain:	n/a	n/a
9	EGR1	chr18:45457769-45458068	K562	blood:	n/a	chr18:45457977-45457992
10	SIN3A	chr18:45455970-45458510	H1-hESC	embryonic stem cell:	n/a	chr18:45456992-45457005
11	ELK1	chr18:45457132-45458253	Hela-S3	cervix:	n/a	n/a
12	MAX	chr18:45456251-45458188	HepG2	liver:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
13	MAX	chr18:45456385-45458222	HCT-116	colon:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
14	USF1	chr18:45457630-45458068	SK-N-SH	brain:	n/a	chr18:45457861-45457872
15	FOXM1	chr18:45457310-45458112	GM12878	blood:	n/a	n/a
16	HCFC1	chr18:45456535-45458436	K562	blood:	n/a	n/a
17	ZNF143	chr18:45456347-45458478	GM12878	blood:	n/a	chr18:45456503-45456513 chr18:45457274-45457284 chr18:45456993-45457003
18	IRF1	chr18:45456767-45458437	K562	blood:	n/a	chr18:45457614-45457628 chr18:45457802-45457816
19	POLR2A	chr18:45456964-45458101	GM12878	blood:	n/a	n/a
20	PML	chr18:45457486-45457977	K562	blood:	n/a	n/a
21	NANOG	chr18:45457144-45457919	H1-hESC	embryonic stem cell:	n/a	n/a
22	CREB1	chr18:45456286-45458221	HepG2	liver:	n/a	n/a
23	HEY1	chr18:45456184-45458004	HepG2	liver:	n/a	chr18:45457438-45457453 chr18:45457436-45457451
24	MAZ	chr18:45456087-45458461	K562	blood:	n/a	chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
25	POLR2A	chr18:45454367-45459190	MCF10A-Er-Src	breast:	n/a	n/a
26	JUND	chr18:45456227-45458157	A549	lung:	n/a	chr18:45457609-45457618 chr18:45456617-45456625 chr18:45457619-45457628 chr18:45457535-45457544 chr18:45457366-45457375 chr18:45457309-45457318
27	SP4	chr18:45457471-45458120	H1-hESC	embryonic stem cell:	n/a	chr18:45457616-45457627
28	MXI1	chr18:45457646-45458409	K562	blood:	n/a	n/a
29	MAX	chr18:45456297-45458478	HepG2	liver:	n/a	chr18:45457863-45457873 chr18:45457862-45457873 chr18:45457862-45457873 chr18:45457861-45457874 chr18:45457862-45457872
30	POLR2A	chr18:45456386-45458067	A549	lung:	n/a	n/a
31	POLR2A	chr18:45456382-45458052	GM12878	blood:	n/a	n/a
32	POLR2A	chr18:45455632-45459226	MCF10A-Er-Src	breast:	n/a	n/a
33	TCF12	chr18:45456207-45458189	ECC-1	luminal epithelium:	n/a	n/a
34	EP300	chr18:45457537-45457958	GM12878	blood:	n/a	n/a
35	ZKSCAN1	chr18:45457252-45458431	Hela-S3	cervix:	n/a	n/a
36	RELA	chr18:45456153-45458434	GM15510	blood:	n/a	chr18:45456318-45456327 chr18:45456318-45456327
37	ZNF143	chr18:45457323-45457877	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr18:45457309-45458677	SK-N-SH	brain:	n/a	n/a
39	JUND	chr18:45456001-45458467	K562	blood:	n/a	chr18:45457609-45457618 chr18:45456617-45456625 chr18:45457619-45457628 chr18:45457535-45457544 chr18:45457366-45457375 chr18:45457309-45457318
40	SP1	chr18:45457196-45458135	A549	lung:	n/a	chr18:45457982-45457994 chr18:45457803-45457813 chr18:45457984-45457993 chr18:45457803-45457813 chr18:45457982-45457994 chr18:45457802-45457814 chr18:45457300-45457321 chr18:45457616-45457628 chr18:45457616-45457627 chr18:45457600-45457621 chr18:45457617-45457631
41	CHD2	chr18:45456053-45458413	Hela-S3	cervix:	n/a	chr18:45457449-45457459 chr18:45457438-45457448
42	PAX5	chr18:45457449-45457930	GM12878	blood:	n/a	chr18:45457698-45457707
43	POLR2A	chr18:45456177-45457974	K562	blood:	n/a	n/a
44	FOXA1	chr18:45457707-45458178	HepG2	liver:	n/a	n/a
45	POLR2A	chr18:45456209-45458371	Raji	blood:	n/a	n/a
46	POLR2A	chr18:45457671-45457976	A549	lung:	n/a	n/a
47	YY1	chr18:45457265-45457905	GM12891	blood:	n/a	n/a
48	POLR2A	chr18:45456147-45458207	GM12892	blood:	n/a	n/a
49	POLR2A	chr18:45456969-45457996	GM12891	blood:	n/a	n/a
50	POLR2A	chr18:45456340-45458198	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:45457609..45458225-chr18:45530268..45531251,3	Hela-S3	cervix:
2	chr18:45457293..45458007-chr19:17416376..17416982,2	Hela-S3	cervix:
3	chr18:45448291..45450129-chr18:45457101..45459149,2	MCF-7	breast:
4	chr18:45422809..45427886-chr18:45455832..45459212,8	MCF-7	breast:
5	chr18:45457568..45458509-chr18:45534238..45535078,2	MCF-7	breast:
6	chr18:45456991..45457971-chr3:142297413..142297998,2	Hela-S3	cervix:
7	chr11:62608798..62609721-chr18:45456983..45457891,3	Hela-S3	cervix:
8	chr18:45457637..45459201-chr18:45523865..45526054,2	MCF-7	breast:
9	chr18:45412211..45417305-chr18:45454331..45458060,5	MCF-7	breast:
10	chr18:45419311..45422107-chr18:45455091..45458226,3	K562	blood:
11	chr18:45455170..45457899-chr18:45935970..45938603,2	K562	blood:
12	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000130312	Chromatin interaction
ENSG00000184828	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10432199	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10853560	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11082638	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11082639	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12604337	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12605333	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12956483	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12968107	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1539872	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1573363	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1613672	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1631576	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17741998	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1787176	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1787193	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787194	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787195	0.82[AMR][1000 genomes]
rs1787196	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787197	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1792653	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792655	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792669	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1792670	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792672	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1792675	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792683	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2000708	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2000709	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012555	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2096932	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2096933	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28548478	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3813068	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4939672	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4940109	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4940110	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4940120	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4940127	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61513611	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62086544	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6507790	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7228393	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7231538	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7232764	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7232893	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7233129	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7236177	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7237544	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7243502	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs729112	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs747952	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs747953	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs765213	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8084915	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8095519	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8097580	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8097912	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8097925	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8099127	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8099681	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs948600	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs948601	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs948603	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs948604	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9946556	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9947494	0.81[AMR][1000 genomes]
rs9950207	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9955626	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9961652	0.82[AMR][1000 genomes]
rs9966637	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9966964	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11874858	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45453600-45458200	Active TSS	GM12878-XiMat	blood
2	chr18:45454600-45458000	Active TSS	Ovary	ovary
3	chr18:45454600-45458200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr18:45454600-45458400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr18:45454600-45458400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr18:45454600-45458600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:45454600-45458600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr18:45454800-45458000	Active TSS	HMEC	breast
9	chr18:45454800-45458200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr18:45454800-45458200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:45454800-45458200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:45454800-45458200	Active TSS	Stomach Smooth Muscle	stomach
13	chr18:45454800-45458400	Active TSS	NHLF	lung
14	chr18:45454800-45458600	Active TSS	K562	blood
15	chr18:45455000-45458000	Active TSS	A549	lung
16	chr18:45455000-45458200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr18:45455000-45458200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr18:45455000-45458200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:45455000-45458200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr18:45455000-45458200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:45455000-45458400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr18:45455000-45458600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:45455000-45458600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr18:45455200-45458000	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr18:45455200-45458000	Active TSS	HepG2	liver
26	chr18:45455200-45458200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr18:45455200-45458200	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr18:45455200-45458200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:45455200-45458200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr18:45455200-45458200	Active TSS	Colon Smooth Muscle	Colon
31	chr18:45455200-45458200	Active TSS	Right Ventricle	heart
32	chr18:45455200-45458200	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr18:45455200-45458400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr18:45455200-45458400	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr18:45455200-45458600	Active TSS	Fetal Kidney	kidney
36	chr18:45455400-45458000	Active TSS	Fetal Intestine Large	intestine
37	chr18:45455600-45458000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr18:45455600-45458000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr18:45455600-45458200	Active TSS	NHDF-Ad	bronchial
40	chr18:45455600-45458400	Active TSS	HSMMtube	muscle
41	chr18:45455800-45458000	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr18:45455800-45458000	Active TSS	NHEK	skin
43	chr18:45455800-45458200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr18:45455800-45458200	Active TSS	Aorta	Aorta
45	chr18:45455800-45458200	Active TSS	Brain Anterior Caudate	brain
46	chr18:45455800-45458200	Active TSS	Psoas Muscle	Psoas
47	chr18:45455800-45458200	Active TSS	Rectal Smooth Muscle	rectum
48	chr18:45455800-45458200	Active TSS	HSMM	muscle
49	chr18:45455800-45458400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr18:45455800-45458600	Active TSS	Pancreatic Islets	Pancreatic Islet

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