Variant report

Variant	rs12457664
Chromosome Location	chr18:45452321-45452322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr18:45452159-45453214	PBDE	blood:	n/a	n/a
2	GATA2	chr18:45452195-45452511	SH-SY5Y	brain:	n/a	n/a
3	USF1	chr18:45452106-45452410	SK-N-SH_RA	brain:	n/a	n/a
4	ZNF384	chr18:45452251-45452347	K562	blood:	n/a	n/a
5	USF1	chr18:45452108-45452389	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr18:45452223-45452455	K562	blood:	n/a	n/a
7	USF1	chr18:45452106-45452348	SK-N-SH_RA	brain:	n/a	n/a
8	USF2	chr18:45452097-45452449	Hela-S3	cervix:	n/a	chr18:45452242-45452253
9	USF1	chr18:45452035-45452472	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:45425101..45428042-chr18:45452196..45454277,2	MCF-7	breast:
2	chr18:45444480..45447818-chr18:45450638..45453118,3	K562	blood:
3	chr18:45451758..45454511-chr18:45455218..45457678,2	MCF-7	breast:
4	chr18:45441870..45444292-chr18:45451454..45453055,2	MCF-7	breast:
5	chr18:45450692..45455196-chr18:45455930..45459309,6	MCF-7	breast:
6	chr18:45452201..45455106-chr18:45476820..45479374,2	MCF-7	breast:

No data

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

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10445485	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10502890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10853560	0.85[CEU][hapmap]
rs11082638	0.85[CEU][hapmap]
rs11082639	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11082641	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11659463	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12458238	0.89[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12604337	0.81[EUR][1000 genomes]
rs12605333	0.83[EUR][1000 genomes]
rs12968107	0.85[CEU][hapmap]
rs12968493	0.93[ASW][hapmap];0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12969725	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1539871	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs1539872	0.85[CEU][hapmap]
rs1573362	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1573363	0.85[CEU][hapmap]
rs1613672	0.82[CEU][hapmap]
rs1631576	0.82[CEU][hapmap]
rs17741998	0.85[CEU][hapmap]
rs1787176	0.82[CEU][hapmap]
rs1787186	0.93[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs1787193	0.82[CEU][hapmap]
rs1787194	0.82[CEU][hapmap]
rs1787196	0.81[AFR][1000 genomes]
rs1787198	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1787199	0.90[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs1792655	0.82[CEU][hapmap]
rs1792658	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs1792666	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1792667	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1792668	0.93[ASW][hapmap];0.89[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1792669	0.85[CEU][hapmap]
rs1792670	0.85[CEU][hapmap]
rs1792671	0.82[CEU][hapmap]
rs1792674	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1792675	0.82[CEU][hapmap]
rs1792684	0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap]
rs1792686	0.81[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs1792687	0.93[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792689	1.00[YRI][hapmap]
rs1942158	0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2000708	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2000709	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2012555	0.85[CEU][hapmap];0.84[LWK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs2096933	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs3813068	0.89[CEU][hapmap]
rs4939672	0.83[EUR][1000 genomes]
rs4940102	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4940109	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4940110	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs57620563	0.99[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6507790	0.92[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6507791	0.85[CEU][hapmap]
rs7228393	0.92[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs7231538	0.85[CEU][hapmap]
rs7233129	0.85[CEU][hapmap]
rs7236177	0.85[CEU][hapmap]
rs7243502	0.82[EUR][1000 genomes]
rs729112	0.85[CEU][hapmap]
rs747952	0.85[CEU][hapmap]
rs747953	0.85[CEU][hapmap]
rs765213	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs8095519	0.96[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs8097580	0.87[CEU][hapmap]
rs8097912	0.85[CEU][hapmap]
rs8097925	0.83[EUR][1000 genomes]
rs8099127	0.85[CEU][hapmap]
rs948601	0.83[EUR][1000 genomes]
rs948602	0.89[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs948603	0.85[CEU][hapmap]
rs948604	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9946556	0.82[CEU][hapmap]
rs9955626	0.85[CEU][hapmap]
rs9966964	0.82[CEU][hapmap]

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	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

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45433200-45455000	Weak transcription	Fetal Stomach	stomach
2	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
3	chr18:45434000-45454600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr18:45435400-45452400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr18:45435600-45455800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr18:45438600-45454600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr18:45438800-45453400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr18:45439000-45452800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr18:45439000-45452800	Weak transcription	Aorta	Aorta
10	chr18:45439000-45456200	Weak transcription	Esophagus	oesophagus
11	chr18:45439000-45456200	Weak transcription	Spleen	Spleen
12	chr18:45439200-45453000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr18:45439200-45453400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr18:45439600-45455400	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:45439800-45452800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:45439800-45454600	Weak transcription	Fetal Intestine Large	intestine
17	chr18:45439800-45456200	Weak transcription	Pancreas	Pancrea
18	chr18:45440000-45452400	Weak transcription	Fetal Intestine Small	intestine
19	chr18:45440600-45452400	Weak transcription	Adipose Nuclei	Adipose
20	chr18:45440600-45452400	Weak transcription	Brain Anterior Caudate	brain
21	chr18:45440800-45452400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr18:45441200-45453000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr18:45442000-45454800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr18:45442400-45452800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr18:45442400-45453400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:45442400-45453600	Weak transcription	NH-A	brain
27	chr18:45442400-45455000	Weak transcription	HSMM	muscle
28	chr18:45442600-45454600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr18:45442800-45454400	Weak transcription	NHDF-Ad	bronchial
30	chr18:45443000-45456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr18:45443600-45455000	Weak transcription	Osteobl	bone
32	chr18:45444400-45454400	Enhancers	Primary T cells from cord blood	blood
33	chr18:45444800-45453200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr18:45444800-45456000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr18:45444800-45456000	Weak transcription	Lung	lung
36	chr18:45445400-45453000	Weak transcription	NHEK	skin
37	chr18:45446000-45455400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr18:45446200-45452400	Weak transcription	Gastric	stomach
39	chr18:45446200-45454400	Weak transcription	Fetal Kidney	kidney
40	chr18:45446200-45455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr18:45446600-45453600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr18:45447600-45452400	Weak transcription	Small Intestine	intestine
43	chr18:45447600-45456000	Weak transcription	Left Ventricle	heart
44	chr18:45448000-45453000	Weak transcription	Brain Angular Gyrus	brain
45	chr18:45448400-45454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:45448600-45453000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr18:45448600-45453600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:45448800-45452400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:45449400-45454800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr18:45450000-45452400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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