Variant report

Variant	rs12804997
Chromosome Location	chr11:86320567-86320568
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86232940..86235698-chr11:86318097..86321251,3	MCF-7	breast:
2	chr11:86165943..86168698-chr11:86319331..86321067,2	MCF-7	breast:
3	chr11:86316496..86321662-chr11:86508610..86513631,11	MCF-7	breast:
4	chr11:86319092..86320819-chr11:86342612..86344114,2	MCF-7	breast:
5	chr11:86318121..86320638-chr11:86509827..86512612,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10501627	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10501628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10898508	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11234707	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11234708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11494278	0.87[AFR][1000 genomes]
rs11606017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11607554	0.92[CEU][hapmap]
rs12361283	0.91[CEU][hapmap]
rs12365092	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12790474	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1540083	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1541308	0.93[ASN][1000 genomes]
rs1541309	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1541310	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1938922	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382935	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4944576	1.00[JPT][hapmap]
rs4944614	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7930619	1.00[JPT][hapmap]

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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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	9 gene(s)	inside rSNPs	diseases
5	nsv898057	chr11:86306401-86335459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv522823	chr11:86317519-86321576	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12804997	CTSC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86308800-86321600	Weak transcription	Left Ventricle	heart
2	chr11:86309400-86321600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:86317400-86321600	Weak transcription	Pancreas	Pancrea
4	chr11:86317800-86320600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:86317800-86320600	Enhancers	HMEC	breast
6	chr11:86318200-86321200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:86318400-86321000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:86318400-86321200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:86318400-86321600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:86318400-86321600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:86318400-86321800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:86319000-86321400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:86319000-86321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:86319000-86321400	Weak transcription	Right Ventricle	heart
15	chr11:86319200-86321000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:86319400-86322000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr11:86319600-86320600	Weak transcription	Fetal Brain Male	brain
18	chr11:86319600-86320600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:86319600-86321400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:86319600-86321400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:86319600-86321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:86319600-86321800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:86319600-86322000	Enhancers	A549	lung
24	chr11:86319600-86328200	Weak transcription	Ovary	ovary
25	chr11:86319800-86321400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:86320000-86321000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:86320000-86321800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:86320000-86322200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:86320000-86325000	Weak transcription	Adipose Nuclei	Adipose
30	chr11:86320000-86330400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:86320200-86321000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:86320200-86321200	Weak transcription	Fetal Heart	heart
33	chr11:86320200-86321400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:86320200-86321800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:86320400-86321400	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:86320400-86321400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:86320400-86321600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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