Variant report

Variant	rs11632941
Chromosome Location	chr15:77533888-77533889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77533789..77536624-chr15:77711955..77714562,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11072643	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1125617	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11630689	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11639314	0.94[ASN][1000 genomes]
rs11853287	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11853460	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854193	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857294	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11858641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1191196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12443386	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900433	0.90[ASN][1000 genomes]
rs12901297	0.80[AMR][1000 genomes]
rs12904088	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907847	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908262	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12909924	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913233	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12914128	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916731	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1473922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1823100	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1867779	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2175941	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28584877	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34591043	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs3743478	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743479	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4243045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4414462	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886511	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886856	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs62008452	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495237	0.86[ASN][1000 genomes]
rs7163503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7177533	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs8024485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8028571	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8037426	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' 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
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11632941	HEXA	cis	cerebellum	SCAN
rs11632941	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:77505800-77559400	Weak transcription	Psoas Muscle	Psoas
3	chr15:77508000-77543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:77511200-77541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:77517400-77559000	Weak transcription	Ovary	ovary
6	chr15:77517600-77543200	Weak transcription	HSMM	muscle
7	chr15:77517600-77545800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:77517800-77535400	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:77517800-77544200	Weak transcription	NHLF	lung
10	chr15:77519400-77551800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:77519600-77551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:77519800-77557200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:77520000-77540000	Weak transcription	HUVEC	blood vessel
14	chr15:77520200-77578800	Weak transcription	Small Intestine	intestine
15	chr15:77523200-77544000	Weak transcription	Pancreas	Pancrea
16	chr15:77526400-77547600	Weak transcription	Liver	Liver
17	chr15:77526600-77538600	Weak transcription	Osteobl	bone
18	chr15:77527000-77559000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:77527000-77576200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr15:77528200-77544200	Weak transcription	NH-A	brain
21	chr15:77528400-77553000	Weak transcription	Aorta	Aorta
22	chr15:77528600-77535600	Weak transcription	Fetal Brain Female	brain
23	chr15:77528600-77544000	Weak transcription	Placenta	Placenta
24	chr15:77528800-77559200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:77528800-77571400	Weak transcription	Right Ventricle	heart
26	chr15:77528800-77574400	Weak transcription	HepG2	liver
27	chr15:77528800-77577200	Weak transcription	Spleen	Spleen
28	chr15:77528800-77579200	Weak transcription	Brain Angular Gyrus	brain
29	chr15:77529000-77540800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:77529000-77543800	Weak transcription	HSMMtube	muscle
31	chr15:77529000-77544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:77529000-77544200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr15:77529000-77548600	Weak transcription	Gastric	stomach
34	chr15:77529200-77534600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:77529200-77535400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:77529200-77538600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:77529200-77540600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:77529200-77540800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:77529200-77541200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:77529200-77544000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:77529200-77544000	Weak transcription	Fetal Lung	lung
42	chr15:77529200-77545800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr15:77529200-77546400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:77529200-77546800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:77529200-77561400	Weak transcription	Primary T cells from cord blood	blood
46	chr15:77529400-77535400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:77529400-77536000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:77529400-77538400	Weak transcription	Fetal Intestine Small	intestine
49	chr15:77529400-77538600	Weak transcription	Fetal Stomach	stomach
50	chr15:77529400-77539800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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