Variant report

Variant	rs7928547
Chromosome Location	chr11:101994051-101994052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:101980088..101982461-chr11:101993738..101996664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137693	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10750632	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750633	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10750634	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10791564	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791565	0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs10895258	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10895261	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895263	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895264	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10895265	0.93[ASN][1000 genomes]
rs10895266	0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs11225134	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225135	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11225139	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11225141	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11225146	0.85[ASN][1000 genomes]
rs11225147	0.84[ASN][1000 genomes]
rs11225149	0.82[EUR][1000 genomes]
rs11225151	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs11603468	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11606471	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607135	0.80[EUR][1000 genomes]
rs12223094	0.80[EUR][1000 genomes]
rs12790160	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12796162	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1365330	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1426392	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1426394	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1834595	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834596	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1893497	0.81[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1895917	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1942680	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1942688	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1942689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1942690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1942691	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003357	0.87[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2019070	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3890538	0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4329661	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4442513	0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4754833	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4754834	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60304309	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61538959	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6590949	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7108698	0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7108820	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7117239	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120363	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123862	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7124280	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126535	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7126944	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7127597	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7128788	0.95[AFR][1000 genomes]
rs7130772	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7483889	0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs7924449	0.80[EUR][1000 genomes]
rs7924737	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7927957	0.80[EUR][1000 genomes]
rs7932563	0.92[AFR][1000 genomes]
rs7938172	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs948737	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9787890	0.81[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	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv898333	chr11:101832670-102079986	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7928547	CASP1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101983400-101998200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:101983600-101998000	Weak transcription	Right Ventricle	heart
3	chr11:101983600-101998200	Weak transcription	Colonic Mucosa	Colon
4	chr11:101983600-102014800	Weak transcription	Pancreas	Pancrea
5	chr11:101985200-101998000	Weak transcription	Gastric	stomach
6	chr11:101985200-102009200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:101986800-101995400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:101986800-101995600	Weak transcription	Right Atrium	heart
9	chr11:101987400-101995000	Weak transcription	Placenta	Placenta
10	chr11:101987400-101996600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:101988800-102009000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:101988800-102009600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:101989600-102015200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:101990000-101995400	Weak transcription	Aorta	Aorta
15	chr11:101990000-101995400	Weak transcription	Esophagus	oesophagus
16	chr11:101990000-101995400	Weak transcription	Left Ventricle	heart
17	chr11:101990000-101995800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:101991000-102009000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:101991000-102010000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:101991400-101995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:101991400-101996600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:101991400-101997200	Weak transcription	Liver	Liver
23	chr11:101991400-101998000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:101991600-101995000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:101991600-101995400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:101991600-101996200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:101991600-102002200	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:101991600-102006000	Weak transcription	NHLF	lung
29	chr11:101991600-102008800	Weak transcription	HSMMtube	muscle
30	chr11:101991600-102012400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:101991600-102015200	Weak transcription	Fetal Kidney	kidney
32	chr11:101991600-102015600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:101991800-101995000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:101991800-101996400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:101991800-101996600	Weak transcription	Fetal Heart	heart
36	chr11:101991800-102001000	Weak transcription	HSMM	muscle
37	chr11:101991800-102001400	Strong transcription	Fetal Stomach	stomach
38	chr11:101992000-101995000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:101992000-101995400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:101992000-101996600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:101992000-101996800	Weak transcription	NH-A	brain
42	chr11:101992000-101999600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:101992200-101995200	Weak transcription	HepG2	liver
44	chr11:101992400-101995000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:101992400-101995400	Weak transcription	HMEC	breast
46	chr11:101992400-101995800	Strong transcription	Fetal Lung	lung
47	chr11:101992400-101997600	Weak transcription	Adipose Nuclei	Adipose
48	chr11:101992600-101995200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:101992600-101995400	Weak transcription	Osteobl	bone
50	chr11:101992600-101995600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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