Variant report

Variant	rs11227248
Chromosome Location	chr11:65428178-65428179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65427470-65428225	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:65427653-65428188	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr11:65424375-65428217	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65423887..65432217-chr11:65622069..65628988,12	K562	blood:
2	chr11:65381571..65386287-chr11:65427993..65433260,8	MCF-7	breast:

Variant related genes	Relation type
RELA	TF binding region
ENSG00000172757	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10896027	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11227249	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227250	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11227261	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1205259	0.81[EUR][1000 genomes]
rs12281400	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2448490	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34007146	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34462081	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930156	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930304	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7944860	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
2	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
3	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
5	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
6	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
7	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
8	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
13	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
14	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
15	nsv897754	chr11:65405300-65436888	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
16	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
17	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11227248	RNASEH2C	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65420800-65429800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65421200-65428800	Strong transcription	Fetal Brain Female	brain
3	chr11:65421200-65429000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:65421200-65429000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:65421200-65429000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:65421200-65429400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:65421400-65428600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:65421400-65428600	Strong transcription	NHEK	skin
9	chr11:65421400-65428800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:65421400-65428800	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr11:65421400-65429000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:65421400-65429200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:65421600-65428200	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr11:65421600-65428600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:65421600-65428600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:65421600-65428800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:65421600-65428800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:65421600-65428800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:65421600-65428800	Strong transcription	Rectal Smooth Muscle	rectum
20	chr11:65421600-65428800	Strong transcription	A549	lung
21	chr11:65421600-65428800	Strong transcription	HSMM	muscle
22	chr11:65421600-65428800	Strong transcription	Osteobl	bone
23	chr11:65421600-65429000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:65421600-65429000	Strong transcription	Lung	lung
25	chr11:65421600-65429200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:65421600-65429200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:65421800-65429000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr11:65421800-65429000	Strong transcription	HSMMtube	muscle
29	chr11:65422000-65428600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:65422000-65428600	Strong transcription	Primary T cells from cord blood	blood
31	chr11:65422000-65428600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:65422000-65428600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:65422000-65428600	Strong transcription	Fetal Stomach	stomach
34	chr11:65422000-65428600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:65422000-65428600	Strong transcription	Thymus	Thymus
36	chr11:65422000-65428600	Strong transcription	NHLF	lung
37	chr11:65422000-65428800	Strong transcription	Brain Angular Gyrus	brain
38	chr11:65422000-65428800	Strong transcription	Ovary	ovary
39	chr11:65422000-65428800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr11:65422200-65428600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:65422200-65428600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:65422200-65428600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr11:65422200-65428600	Strong transcription	Brain Substantia Nigra	brain
44	chr11:65422200-65428800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:65422200-65428800	Strong transcription	Fetal Lung	lung
46	chr11:65422400-65428600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:65422400-65428600	Strong transcription	Left Ventricle	heart
48	chr11:65422400-65428600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr11:65422400-65428600	Strong transcription	NHDF-Ad	bronchial
50	chr11:65422400-65429000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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