Variant report

Variant	rs11804220
Chromosome Location	chr1:46840238-46840239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11211267	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11802856	1.00[EUR][1000 genomes]
rs11804982	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086460	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12096333	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35563048	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3931457	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57638901	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6703596	1.00[EUR][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS 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	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
7	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46807600-46844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46809200-46848600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:46828200-46845400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:46828600-46843800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:46829200-46840400	Weak transcription	Gastric	stomach
6	chr1:46829200-46846400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:46829200-46847200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:46829200-46847600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:46829200-46848000	Weak transcription	Ovary	ovary
10	chr1:46829400-46859400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:46830200-46842000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:46830600-46840600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:46830600-46848800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:46830800-46841000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:46831400-46840400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:46833400-46845600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:46834600-46840400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:46834600-46840600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:46834600-46847800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:46834600-46859600	Weak transcription	Psoas Muscle	Psoas
21	chr1:46834800-46840400	Weak transcription	Thymus	Thymus
22	chr1:46834800-46840800	Weak transcription	Fetal Intestine Large	intestine
23	chr1:46834800-46842600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:46834800-46844400	Weak transcription	Lung	lung
25	chr1:46834800-46844800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:46834800-46846200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:46834800-46846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:46834800-46847600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:46834800-46848600	Weak transcription	Fetal Stomach	stomach
30	chr1:46834800-46853800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:46835000-46840800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:46835000-46841000	Weak transcription	Liver	Liver
33	chr1:46835000-46841400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:46835000-46847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:46835400-46845800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:46835600-46840600	Weak transcription	Fetal Brain Female	brain
37	chr1:46836000-46847200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:46836200-46845600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:46836200-46845600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:46836200-46845800	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:46836200-46859400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:46836600-46843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:46836600-46848800	Weak transcription	Primary T cells from cord blood	blood
44	chr1:46836800-46848800	Weak transcription	Adipose Nuclei	Adipose
45	chr1:46837800-46840800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:46839400-46841000	Weak transcription	Dnd41	blood
47	chr1:46839400-46842000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:46839400-46847600	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:46839400-46848400	Weak transcription	Placenta	Placenta
50	chr1:46839400-46848800	Weak transcription	Fetal Intestine Small	intestine

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