Variant report

Variant	rs10502890
Chromosome Location	chr18:45462167-45462168
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	chr18:45461971-45462176	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:45455293..45460284-chr18:45461737..45465980,6	K562	blood:
2	chr18:45456285..45458398-chr18:45460688..45463962,5	MCF-7	breast:
3	chr18:45423330..45425218-chr18:45460389..45462320,2	K562	blood:

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

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10445485	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10853560	0.85[CEU][hapmap]
rs11082638	0.85[CEU][hapmap]
rs11082639	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11082641	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11659463	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12457664	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]
rs12458238	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12605333	0.82[EUR][1000 genomes]
rs12968107	0.85[CEU][hapmap]
rs12968493	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[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];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12969725	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[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];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539871	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs1539872	0.85[CEU][hapmap]
rs1573362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[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];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787199	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1792655	0.82[CEU][hapmap]
rs1792658	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs1792666	0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap]
rs1792667	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792668	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[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];0.88[EUR][1000 genomes];0.90[ASN][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];0.85[CHD][hapmap];1.00[GIH][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];0.86[EUR][1000 genomes]
rs1792675	0.82[CEU][hapmap]
rs1792684	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[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];0.87[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[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];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792689	1.00[YRI][hapmap]
rs1942158	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[ASN][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];0.82[EUR][1000 genomes]
rs3813068	0.89[CEU][hapmap]
rs4939672	0.82[EUR][1000 genomes]
rs4940102	0.89[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4940109	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4940110	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs57620563	0.99[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6507790	0.92[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6507791	0.85[CEU][hapmap]
rs7228393	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7231538	0.85[CEU][hapmap]
rs7233129	0.85[CEU][hapmap]
rs7236177	0.85[CEU][hapmap]
rs7243502	0.81[EUR][1000 genomes]
rs729112	0.85[CEU][hapmap]
rs747952	0.85[CEU][hapmap]
rs747953	0.85[CEU][hapmap]
rs765213	0.92[CEU][hapmap]
rs8095519	0.96[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs8097580	0.87[CEU][hapmap]
rs8097912	0.85[CEU][hapmap]
rs8097925	0.81[EUR][1000 genomes]
rs8099127	0.85[CEU][hapmap]
rs948601	0.82[EUR][1000 genomes]
rs948602	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs948603	0.85[CEU][hapmap]
rs948604	0.96[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9946556	0.82[CEU][hapmap]
rs9955626	0.85[CEU][hapmap]
rs9966964	0.82[CEU][hapmap]

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	esv3358262	chr18:45460344-45464204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10502890	SMAD2	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 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	chr18:45458400-45463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr18:45458400-45463400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr18:45458600-45462200	Weak transcription	Brain Angular Gyrus	brain
5	chr18:45458600-45462200	Weak transcription	Brain Anterior Caudate	brain
6	chr18:45458600-45463200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr18:45458600-45463400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr18:45458800-45463400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr18:45458800-45463600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr18:45459000-45462400	Weak transcription	Primary T cells from cord blood	blood
11	chr18:45459000-45463200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr18:45459000-45464800	Weak transcription	Pancreas	Pancrea
13	chr18:45459400-45462400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr18:45459600-45462200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr18:45459600-45462200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr18:45459600-45471600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr18:45459800-45462200	Weak transcription	Fetal Thymus	thymus
18	chr18:45459800-45463000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr18:45459800-45463200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr18:45459800-45464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:45459800-45464600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:45460400-45462600	Weak transcription	Thymus	Thymus
23	chr18:45460600-45462200	Weak transcription	Dnd41	blood
24	chr18:45461000-45463200	Weak transcription	Hela-S3	cervix
25	chr18:45461000-45463600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr18:45461600-45462800	Enhancers	Brain Substantia Nigra	brain
27	chr18:45461800-45462200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:45461800-45462800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr18:45461800-45463400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr18:45462000-45462600	Enhancers	Brain Germinal Matrix	brain
31	chr18:45462000-45462800	Enhancers	Brain Cingulate Gyrus	brain
32	chr18:45462000-45462800	Enhancers	Brain Hippocampus Middle	brain
33	chr18:45462000-45463200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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