Variant report

Variant	rs4420227
Chromosome Location	chr11:102036484-102036485
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	chr11:101980726..101983626-chr11:102035449..102038162,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137693	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10791566	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10791569	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10895269	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895270	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10895271	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs11225153	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11225155	0.91[ASN][1000 genomes]
rs11225169	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs11605954	0.92[MEX][hapmap]
rs12222063	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820454	0.87[EUR][1000 genomes]
rs1893498	0.80[MEX][hapmap]
rs1942683	1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs2114308	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187525	0.83[MEX][hapmap]
rs2846836	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2846837	0.83[EUR][1000 genomes]
rs4561174	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4754836	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61893575	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104685	0.88[EUR][1000 genomes]
rs7106107	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs7107909	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs7110355	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[TSI][hapmap];0.87[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4420227	CASP1	cis	parietal	SCAN
rs4420227	CASP5	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102010400-102039000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:102020400-102049000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:102025600-102039000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:102026400-102059400	Weak transcription	Fetal Brain Male	brain
5	chr11:102026600-102045400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:102027800-102037200	Weak transcription	Fetal Kidney	kidney
7	chr11:102028000-102062800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:102028600-102039000	Weak transcription	NHLF	lung
9	chr11:102028600-102055200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:102029200-102045400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:102029200-102067600	Weak transcription	HSMMtube	muscle
12	chr11:102029400-102042000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:102029400-102050000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:102030200-102041400	Weak transcription	HUVEC	blood vessel
15	chr11:102030200-102048600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:102030600-102042200	Weak transcription	Stomach Mucosa	stomach
17	chr11:102031200-102043400	Weak transcription	Pancreas	Pancrea
18	chr11:102031600-102037200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:102031600-102039200	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:102031800-102042600	Weak transcription	Aorta	Aorta
21	chr11:102032600-102038000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:102033000-102037600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:102033000-102037800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:102033200-102036600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:102033200-102036800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:102033200-102037000	Strong transcription	Liver	Liver
27	chr11:102033200-102037400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:102033400-102036800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:102033400-102036800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:102033400-102037000	Strong transcription	Fetal Lung	lung
31	chr11:102033400-102037200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:102033400-102037800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:102033400-102042800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:102033400-102045600	Weak transcription	Spleen	Spleen
35	chr11:102033400-102061000	Weak transcription	Right Ventricle	heart
36	chr11:102033600-102037600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:102033800-102037000	Strong transcription	NHDF-Ad	bronchial
38	chr11:102033800-102038000	Strong transcription	HSMM	muscle
39	chr11:102034400-102036600	Weak transcription	Fetal Heart	heart
40	chr11:102034400-102038600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:102034400-102039000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:102034400-102055200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:102034400-102057200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:102034600-102039000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:102034600-102039200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:102034600-102040800	Weak transcription	Left Ventricle	heart
47	chr11:102034600-102040800	Weak transcription	A549	lung
48	chr11:102034600-102042200	Weak transcription	Adipose Nuclei	Adipose
49	chr11:102034600-102042600	Weak transcription	Placenta	Placenta
50	chr11:102034600-102042800	Weak transcription	Esophagus	oesophagus

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