Variant report

Variant	rs2000709
Chromosome Location	chr18:45459514-45459515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:45459245-45459661	K562	blood:	n/a	n/a
2	POLR2A	chr18:45459476-45459665	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr18:45455600-45459758	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:45458829..45459660-chr18:45523676..45524233,2	MCF-7	breast:
2	chr18:45458331..45460939-chr18:45561622..45564314,2	K562	blood:
3	chr18:45457936..45459581-chr18:45522909..45525211,2	K562	blood:
4	chr18:45458995..45459538-chr18:45548712..45549533,2	MCF-7	breast:
5	chr18:45458884..45459566-chr18:45534298..45534837,2	MCF-7	breast:
6	chr18:45300220..45301757-chr18:45459466..45461739,2	MCF-7	breast:
7	chr18:45458870..45459566-chr18:45548825..45549722,2	MCF-7	breast:
8	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:

No data

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

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10432199	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10502890	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10853560	0.82[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11082638	0.85[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11082639	0.93[CEU][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11082641	0.89[CEU][hapmap]
rs11874858	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12457664	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12604337	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12605333	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12956483	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12968107	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12968493	0.81[CEU][hapmap]
rs12969725	0.81[CEU][hapmap]
rs1539871	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1539872	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1573362	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs1573363	0.82[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1613672	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1631576	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17741998	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787176	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787185	0.91[JPT][hapmap]
rs1787193	0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787194	0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787196	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1787197	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1792653	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1792655	0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1792668	0.81[CEU][hapmap]
rs1792669	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1792670	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792671	0.91[JPT][hapmap]
rs1792672	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1792675	0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1792679	0.91[JPT][hapmap]
rs1792681	0.81[JPT][hapmap]
rs1792682	0.91[JPT][hapmap]
rs1792683	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1792686	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs1981	0.90[JPT][hapmap]
rs2000708	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2012555	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2096932	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2096933	0.96[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28548478	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3813068	0.89[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4939672	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940110	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940120	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940127	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61513611	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62086544	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6507790	0.92[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6507791	0.82[CEU][hapmap]
rs7228393	0.92[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7231538	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7232764	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7232893	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7233129	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7236177	0.85[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7237544	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7243502	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs729112	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs747952	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs747953	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs765213	0.93[CEU][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8084915	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8095519	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8097580	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8097912	0.82[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8097925	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8099127	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8099681	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs948600	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs948601	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs948603	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs948604	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9946556	0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9947494	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9950207	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9955626	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9961652	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9966637	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9966964	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][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	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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45458200-45463400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr18:45458400-45459600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:45458400-45459800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr18:45458400-45459800	Weak transcription	Spleen	Spleen
5	chr18:45458400-45461000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:45458400-45461800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr18:45458400-45463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr18:45458400-45463400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr18:45458600-45459600	Enhancers	Primary hematopoietic stem cells	blood
10	chr18:45458600-45459600	Enhancers	Adipose Nuclei	Adipose
11	chr18:45458600-45459600	Enhancers	HepG2	liver
12	chr18:45458600-45459600	Enhancers	K562	blood
13	chr18:45458600-45459800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr18:45458600-45459800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr18:45458600-45459800	Enhancers	Fetal Kidney	kidney
16	chr18:45458600-45459800	Enhancers	Fetal Thymus	thymus
17	chr18:45458600-45460600	Enhancers	A549	lung
18	chr18:45458600-45462000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr18:45458600-45462000	Weak transcription	Brain Hippocampus Middle	brain
20	chr18:45458600-45462200	Weak transcription	Brain Angular Gyrus	brain
21	chr18:45458600-45462200	Weak transcription	Brain Anterior Caudate	brain
22	chr18:45458600-45463200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr18:45458600-45463400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr18:45458800-45459600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr18:45458800-45459800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr18:45458800-45459800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr18:45458800-45459800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr18:45458800-45459800	Enhancers	Stomach Mucosa	stomach
29	chr18:45458800-45459800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr18:45458800-45460400	Enhancers	Thymus	Thymus
31	chr18:45458800-45460600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr18:45458800-45461000	Enhancers	Hela-S3	cervix
33	chr18:45458800-45461600	Weak transcription	Brain Substantia Nigra	brain
34	chr18:45458800-45461800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:45458800-45463400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr18:45458800-45463600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr18:45459000-45460600	Enhancers	Dnd41	blood
38	chr18:45459000-45462400	Weak transcription	Primary T cells from cord blood	blood
39	chr18:45459000-45463200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr18:45459000-45464800	Weak transcription	Pancreas	Pancrea
41	chr18:45459200-45459600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr18:45459400-45459600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr18:45459400-45459600	Enhancers	Gastric	stomach
44	chr18:45459400-45460200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr18:45459400-45462400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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