Variant report

Variant	rs3807490
Chromosome Location	chr7:16802589-16802590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16792031..16793586-chr7:16802344..16804662,2	MCF-7	breast:
2	chr7:16796604..16799522-chr7:16799940..16802682,3	MCF-7	breast:
3	chr7:16794917..16796909-chr7:16801074..16804000,3	K562	blood:
4	chr7:16783316..16786231-chr7:16801577..16804005,2	K562	blood:
5	chr7:16800951..16805401-chr7:16805504..16810552,5	K562	blood:

Variant related genes	Relation type
ENSG00000106537	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10233465	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10238328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1149519	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1149524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1149526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12530923	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs12535558	0.95[ASN][1000 genomes]
rs13232235	0.84[ASN][1000 genomes]
rs13244013	1.00[ASN][1000 genomes]
rs1997114	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1997115	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2085706	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290836	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2290837	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs34614062	0.95[ASN][1000 genomes]
rs3779051	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807492	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3807509	0.84[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs3823652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4400279	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4721535	0.91[ASN][1000 genomes]
rs4721536	0.90[ASN][1000 genomes]
rs4721538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4721539	0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs55802535	0.87[ASN][1000 genomes]
rs62441050	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6461275	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6942785	0.81[AMR][1000 genomes]
rs6951449	0.85[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs6962578	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6975847	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6980298	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706055	0.91[ASN][1000 genomes]
rs73299615	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7781646	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7809197	0.92[ASN][1000 genomes]
rs818803	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818804	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024059	chr7:16639432-16836425	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3807490	TWIST1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16795000-16804200	Weak transcription	HUVEC	blood vessel
2	chr7:16795000-16806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:16795000-16810200	Weak transcription	HMEC	breast
4	chr7:16795000-16810400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:16795000-16828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:16795200-16810000	Weak transcription	NHEK	skin
7	chr7:16795200-16810600	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:16795400-16813000	Weak transcription	Right Ventricle	heart
9	chr7:16796200-16804600	Weak transcription	Pancreas	Pancrea
10	chr7:16796200-16806400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:16796400-16810200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:16796600-16803600	Weak transcription	Brain Anterior Caudate	brain
13	chr7:16796600-16804400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:16796600-16810400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:16796600-16816200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:16799000-16803200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:16799000-16807800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:16799000-16810400	Weak transcription	K562	blood
19	chr7:16799600-16802600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:16799600-16810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:16799600-16813000	Weak transcription	Stomach Mucosa	stomach
22	chr7:16799800-16803000	Weak transcription	Gastric	stomach
23	chr7:16799800-16804600	Weak transcription	Left Ventricle	heart
24	chr7:16800200-16802800	Genic enhancers	Primary B cells from cord blood	blood
25	chr7:16800200-16803200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr7:16800400-16802800	Enhancers	Fetal Intestine Large	intestine
27	chr7:16800600-16825600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:16800800-16803000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:16801400-16802600	Weak transcription	Fetal Intestine Small	intestine
30	chr7:16801400-16810600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:16801600-16811200	Weak transcription	Spleen	Spleen
32	chr7:16801800-16802800	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr7:16802000-16802600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr7:16802200-16804600	Weak transcription	Small Intestine	intestine
35	chr7:16802200-16810800	Weak transcription	Fetal Heart	heart
36	chr7:16802400-16803600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:16802400-16804800	Weak transcription	Rectal Mucosa Donor 29	rectum

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