Variant report

Variant	rs4754833
Chromosome Location	chr11:102017719-102017720
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	chr11:102010849..102012537-chr11:102015690..102017835,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10750632	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10750633	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10750634	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791564	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791565	0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895258	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895259	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895261	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895262	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10895263	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10895264	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895265	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895266	0.87[CHB][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11225134	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11225135	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11225139	0.81[ASN][1000 genomes]
rs11225141	0.80[EUR][1000 genomes]
rs11225146	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225147	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11225149	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11225151	0.87[CHB][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11603468	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11605954	0.87[GIH][hapmap]
rs11606471	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11607135	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12223094	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12790160	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12796162	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1365330	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1426392	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1426394	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1834595	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1834596	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893497	0.81[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1893498	0.87[GIH][hapmap]
rs1895917	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1942680	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1942688	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1942689	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]
rs1942690	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1942691	0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2003357	0.87[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2019070	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2187525	0.87[GIH][hapmap]
rs3890538	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4329661	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4442513	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4754834	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60304309	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61538959	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6590949	0.82[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7108698	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7108820	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7117239	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7120067	0.94[GIH][hapmap]
rs7120363	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7123862	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7124280	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7126535	0.82[ASN][1000 genomes]
rs7126944	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7127597	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7130772	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7483889	0.87[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7924449	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7924737	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7927957	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7928547	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]
rs7938172	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs948737	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9787890	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4754833	CASP1	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101998600-102033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:101998600-102034200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr11:102000800-102034000	Weak transcription	Lung	lung
4	chr11:102005800-102033000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:102010200-102032400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:102010400-102020800	Weak transcription	Left Ventricle	heart
7	chr11:102010400-102023000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:102010400-102039000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:102011800-102019000	Enhancers	Fetal Heart	heart
10	chr11:102012600-102028600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:102012600-102034200	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:102013800-102019000	Enhancers	HepG2	liver
13	chr11:102014400-102018000	Enhancers	Liver	Liver
14	chr11:102014600-102023000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:102014800-102028400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:102015000-102021600	Weak transcription	Gastric	stomach
17	chr11:102015400-102018400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:102015400-102022000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:102015800-102019000	Enhancers	Fetal Lung	lung
20	chr11:102015800-102021600	Weak transcription	Psoas Muscle	Psoas
21	chr11:102015800-102022400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:102015800-102023400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:102015800-102033200	Weak transcription	Spleen	Spleen
24	chr11:102016000-102017800	Enhancers	Hela-S3	cervix
25	chr11:102016000-102021600	Weak transcription	Right Ventricle	heart
26	chr11:102016000-102021800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:102016000-102022600	Weak transcription	Right Atrium	heart
28	chr11:102016000-102022600	Weak transcription	NHEK	skin
29	chr11:102016000-102023600	Weak transcription	Small Intestine	intestine
30	chr11:102016000-102026200	Weak transcription	HMEC	breast
31	chr11:102016000-102028800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:102016000-102033200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:102016200-102017800	Weak transcription	A549	lung
34	chr11:102016200-102017800	Weak transcription	NHDF-Ad	bronchial
35	chr11:102016200-102018200	Weak transcription	Brain Angular Gyrus	brain
36	chr11:102016200-102020200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:102016200-102022000	Weak transcription	NHLF	lung
38	chr11:102016200-102025400	Weak transcription	Fetal Kidney	kidney
39	chr11:102016200-102026200	Weak transcription	HUVEC	blood vessel
40	chr11:102016200-102026800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:102016200-102027400	Weak transcription	Fetal Intestine Small	intestine
42	chr11:102016200-102027600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:102016200-102027800	Weak transcription	Fetal Intestine Large	intestine
44	chr11:102016200-102027800	Weak transcription	NH-A	brain
45	chr11:102016400-102018000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:102016400-102022600	Weak transcription	Osteobl	bone
47	chr11:102016600-102018600	Strong transcription	HSMM	muscle
48	chr11:102016600-102018800	Weak transcription	Colon Smooth Muscle	Colon
49	chr11:102016800-102018000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:102016800-102018200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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