Variant report

Variant	rs11856674
Chromosome Location	chr15:57819183-57819184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57632756..57633581-chr15:57818988..57820292,4	MCF-7	breast:
2	chr15:57631137..57633998-chr15:57818191..57820623,2	K562	blood:
3	chr15:57817814..57819834-chr15:57824294..57826002,2	K562	blood:
4	chr15:57632542..57633554-chr15:57819095..57820390,12	K562	blood:
5	chr15:57637629..57639520-chr15:57818149..57819741,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11856034	0.82[MEX][hapmap]
rs12439291	0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs12439292	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs12439665	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439793	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620402	0.81[CHD][hapmap]
rs1623697	0.81[CHD][hapmap]
rs1666573	0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820431	1.00[ASW][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820437	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820449	0.88[ASN][1000 genomes]
rs17820461	0.90[ASN][1000 genomes]
rs17820467	0.90[ASN][1000 genomes]
rs2131730	0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs2131731	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs2270488	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2279606	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2934418	0.90[ASN][1000 genomes]
rs3742963	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs3742964	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4774961	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4774962	0.92[ASN][1000 genomes]
rs55777040	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs55916627	0.92[ASN][1000 genomes]
rs55952634	0.92[ASN][1000 genomes]
rs56362917	0.92[ASN][1000 genomes]
rs59368768	0.92[ASN][1000 genomes]
rs66802357	0.82[ASN][1000 genomes]
rs67336499	0.92[ASN][1000 genomes]
rs7166305	0.92[ASN][1000 genomes]
rs7171354	0.81[ASN][1000 genomes]
rs7171360	0.92[ASN][1000 genomes]
rs72741522	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741528	0.90[ASN][1000 genomes]
rs8025786	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937248	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11856674	TMOD3	cis	parietal	SCAN
rs11856674	CCNB2	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57797000-57827200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:57802000-57819600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:57802800-57822600	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:57803200-57819400	Weak transcription	Ovary	ovary
6	chr15:57803200-57842800	Weak transcription	Aorta	Aorta
7	chr15:57811000-57827800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:57811200-57819400	Weak transcription	Fetal Intestine Small	intestine
9	chr15:57812400-57819400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:57814600-57819400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:57814600-57819400	Weak transcription	Brain Substantia Nigra	brain
12	chr15:57814600-57819600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:57814600-57819600	Strong transcription	Liver	Liver
14	chr15:57814800-57819400	Weak transcription	Brain Anterior Caudate	brain
15	chr15:57814800-57819400	Weak transcription	Fetal Lung	lung
16	chr15:57814800-57819400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:57814800-57819400	Weak transcription	Right Atrium	heart
18	chr15:57814800-57819600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:57815200-57819600	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:57815200-57819600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:57815400-57819400	Weak transcription	Fetal Kidney	kidney
22	chr15:57816000-57819400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:57816200-57819600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:57816800-57819400	Weak transcription	Stomach Mucosa	stomach
25	chr15:57816800-57819600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:57816800-57820800	Weak transcription	Gastric	stomach
27	chr15:57817000-57820800	Weak transcription	HepG2	liver
28	chr15:57817000-57826600	Weak transcription	Lung	lung
29	chr15:57817200-57819400	Weak transcription	Fetal Stomach	stomach
30	chr15:57817200-57819800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr15:57817200-57819800	Enhancers	HUVEC	blood vessel
32	chr15:57817200-57820600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:57817200-57820800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr15:57817200-57821000	Weak transcription	Placenta	Placenta
35	chr15:57817200-57827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:57817400-57819400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:57817800-57819400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:57817800-57820200	Enhancers	Fetal Heart	heart
39	chr15:57818000-57819400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:57818000-57819800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:57818000-57819800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:57818000-57820000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:57818200-57820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:57818400-57819400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:57818400-57820000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:57818600-57819800	Enhancers	NH-A	brain
47	chr15:57818800-57819200	Weak transcription	NHDF-Ad	bronchial
48	chr15:57818800-57819800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:57818800-57819800	Enhancers	Fetal Intestine Large	intestine
50	chr15:57819000-57819200	Enhancers	Esophagus	oesophagus

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