Variant report

Variant	rs2411299
Chromosome Location	chr15:39959900-39959901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:39959771..39962008-chr15:40012951..40014930,2	MCF-7	breast:
2	chr15:39920700..39923129-chr15:39958970..39962199,4	MCF-7	breast:
3	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
4	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
5	chr15:39890163..39892186-chr15:39958834..39961393,2	MCF-7	breast:
6	chr15:39892943..39897047-chr15:39958260..39961815,3	MCF-7	breast:
7	chr15:39930109..39933577-chr15:39957965..39961029,3	MCF-7	breast:
8	chr15:39878927..39880641-chr15:39959246..39961103,2	MCF-7	breast:
9	chr15:39880858..39882664-chr15:39957984..39960909,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10520137	0.81[EUR][1000 genomes]
rs1105159	0.86[CHB][hapmap]
rs11070221	0.83[EUR][1000 genomes]
rs11070222	0.83[EUR][1000 genomes]
rs11070223	0.84[EUR][1000 genomes]
rs11070224	0.83[EUR][1000 genomes]
rs11070225	0.84[EUR][1000 genomes]
rs11070226	0.93[EUR][1000 genomes]
rs11070227	0.93[EUR][1000 genomes]
rs11070228	0.93[EUR][1000 genomes]
rs11070231	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11630406	0.93[EUR][1000 genomes]
rs11631820	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11631824	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11632117	0.90[EUR][1000 genomes]
rs11632879	0.90[EUR][1000 genomes]
rs11635103	0.93[EUR][1000 genomes]
rs11636823	0.93[EUR][1000 genomes]
rs11638041	0.90[EUR][1000 genomes]
rs11638558	0.90[EUR][1000 genomes]
rs11852591	0.93[EUR][1000 genomes]
rs11852649	0.93[EUR][1000 genomes]
rs11854797	0.95[YRI][hapmap]
rs11855487	0.88[EUR][1000 genomes]
rs11856971	0.93[EUR][1000 genomes]
rs11857819	0.83[EUR][1000 genomes]
rs12050804	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12899323	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12900024	0.84[ASN][1000 genomes]
rs12900583	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs12901142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903514	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908846	0.84[EUR][1000 genomes]
rs12911549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911999	0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs16969386	0.84[EUR][1000 genomes]
rs16969395	0.84[EUR][1000 genomes]
rs16969410	0.83[EUR][1000 genomes]
rs16969426	0.90[EUR][1000 genomes]
rs16969429	0.90[EUR][1000 genomes]
rs16969451	0.90[EUR][1000 genomes]
rs16969459	0.90[EUR][1000 genomes]
rs16969475	0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs16969478	0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs172104	0.83[JPT][hapmap]
rs1876853	0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs1906152	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1906155	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1906156	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1994379	0.91[CHB][hapmap]
rs2129459	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2411300	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2411301	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs2411307	0.90[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs2411308	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411309	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411310	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2411311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411312	1.00[CEU][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs2411313	0.93[EUR][1000 genomes]
rs2411314	0.93[EUR][1000 genomes]
rs2412413	0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2412414	0.90[EUR][1000 genomes]
rs2412415	0.90[EUR][1000 genomes]
rs2412416	0.90[EUR][1000 genomes]
rs2412417	0.90[EUR][1000 genomes]
rs2412419	0.82[EUR][1000 genomes]
rs2412420	0.82[EUR][1000 genomes]
rs2631697	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631700	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2631702	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631704	0.88[ASN][1000 genomes]
rs2631705	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2631710	0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2664125	0.88[ASN][1000 genomes]
rs2664133	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2664135	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs28437905	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28581473	0.94[ASN][1000 genomes]
rs2898685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898686	0.89[EUR][1000 genomes]
rs2898687	0.85[TSI][hapmap]
rs2898688	0.90[EUR][1000 genomes]
rs2898962	0.90[EUR][1000 genomes]
rs3103065	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4319738	0.94[ASN][1000 genomes]
rs4349120	0.90[EUR][1000 genomes]
rs4429263	0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4476148	0.89[ASN][1000 genomes]
rs4479205	0.88[EUR][1000 genomes]
rs4480779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4493017	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4505280	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4526992	0.95[EUR][1000 genomes]
rs4547308	0.90[EUR][1000 genomes]
rs4572354	0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4583211	0.95[EUR][1000 genomes]
rs4591113	0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4606692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4628934	0.90[EUR][1000 genomes]
rs4924376	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4924377	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs56938133	0.83[EUR][1000 genomes]
rs59449051	0.95[EUR][1000 genomes]
rs60164392	0.90[EUR][1000 genomes]
rs60195210	0.90[EUR][1000 genomes]
rs61130460	0.93[EUR][1000 genomes]
rs61439563	0.95[EUR][1000 genomes]
rs61568256	0.93[EUR][1000 genomes]
rs6492909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492910	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6492911	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs67239630	0.82[EUR][1000 genomes]
rs68183224	0.85[ASN][1000 genomes]
rs7162070	0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7162781	0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs7167100	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167184	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7168755	0.90[EUR][1000 genomes]
rs7169478	0.85[EUR][1000 genomes]
rs7169574	0.85[EUR][1000 genomes]
rs7177324	0.82[EUR][1000 genomes]
rs7177857	0.84[ASN][1000 genomes]
rs7179013	0.90[CHB][hapmap]
rs7179608	0.93[EUR][1000 genomes]
rs72725079	0.90[EUR][1000 genomes]
rs72725080	0.90[EUR][1000 genomes]
rs72725084	0.90[EUR][1000 genomes]
rs72725093	0.93[EUR][1000 genomes]
rs72725101	0.93[EUR][1000 genomes]
rs8026916	0.90[EUR][1000 genomes]
rs8029602	0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs8032035	0.83[EUR][1000 genomes]
rs8032289	0.90[EUR][1000 genomes]
rs8033902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034543	0.94[ASN][1000 genomes]
rs8034885	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035354	0.94[ASN][1000 genomes]
rs8036226	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042068	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884584	0.85[TSI][hapmap];0.95[EUR][1000 genomes]
rs9302102	0.83[EUR][1000 genomes]
rs937960	0.90[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs951358	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9672572	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9806647	0.82[EUR][1000 genomes]
rs999393	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2411299	THBS1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39955800-39960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:39955800-39960200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr15:39956000-39960200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:39956600-39960000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr15:39956800-39961400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:39957200-39961000	Enhancers	HSMMtube	muscle
7	chr15:39957600-39961200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:39958000-39960200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:39958200-39960200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:39958200-39961000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:39958400-39960000	Enhancers	Fetal Kidney	kidney
12	chr15:39958400-39960200	Enhancers	HSMM	muscle
13	chr15:39958600-39960200	Enhancers	Colon Smooth Muscle	Colon
14	chr15:39958800-39960000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:39958800-39960000	Enhancers	Fetal Stomach	stomach
16	chr15:39958800-39960000	Enhancers	Stomach Smooth Muscle	stomach
17	chr15:39958800-39960200	Enhancers	NHDF-Ad	bronchial
18	chr15:39959000-39960000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:39959000-39960200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr15:39959200-39960000	Enhancers	Right Atrium	heart
21	chr15:39959200-39960200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:39959200-39960200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:39959200-39960400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr15:39959200-39960800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:39959200-39961200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:39959400-39960800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:39959400-39962800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:39959600-39960200	Enhancers	Spleen	Spleen
29	chr15:39959800-39960800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:39959800-39960800	Weak transcription	Fetal Lung	lung
31	chr15:39959800-39960800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:39959800-39961400	Enhancers	Liver	Liver
33	chr15:39959800-39961600	Weak transcription	Aorta	Aorta

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