Variant report

Variant	rs541091
Chromosome Location	chr6:160770552-160770553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10945670	0.82[EUR][1000 genomes]
rs1317652	0.82[EUR][1000 genomes]
rs1605963	0.82[EUR][1000 genomes]
rs1605964	0.82[EUR][1000 genomes]
rs1605965	0.87[ASN][1000 genomes]
rs2136676	0.82[EUR][1000 genomes]
rs2313453	0.82[EUR][1000 genomes]
rs2872317	0.82[EUR][1000 genomes]
rs3105748	0.82[EUR][1000 genomes]
rs3105749	0.82[EUR][1000 genomes]
rs3105752	0.82[EUR][1000 genomes]
rs3123633	0.83[EUR][1000 genomes]
rs3123634	0.82[EUR][1000 genomes]
rs3127574	0.83[EUR][1000 genomes]
rs316172	0.85[ASN][1000 genomes]
rs316177	0.84[ASN][1000 genomes]
rs366608	0.86[ASN][1000 genomes]
rs367213	0.85[ASN][1000 genomes]
rs372665	0.85[ASN][1000 genomes]
rs377551	0.91[ASN][1000 genomes]
rs383420	0.85[ASN][1000 genomes]
rs394487	0.91[ASN][1000 genomes]
rs396843	0.85[ASN][1000 genomes]
rs401746	0.84[ASN][1000 genomes]
rs405405	0.91[ASN][1000 genomes]
rs416879	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4235926	0.82[EUR][1000 genomes]
rs423961	0.85[ASN][1000 genomes]
rs425983	0.85[ASN][1000 genomes]
rs431747	0.86[ASN][1000 genomes]
rs435421	0.86[ASN][1000 genomes]
rs445849	0.86[ASN][1000 genomes]
rs4709425	0.82[EUR][1000 genomes]
rs4709426	0.81[EUR][1000 genomes]
rs474513	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486339	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486359	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487060	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487152	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490275	0.86[ASN][1000 genomes]
rs501470	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs505870	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506823	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509707	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518295	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs519118	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520685	0.86[ASN][1000 genomes]
rs520829	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537937	0.86[ASN][1000 genomes]
rs539298	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs539958	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs543159	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547290	0.85[ASN][1000 genomes]
rs555754	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs569919	0.85[ASN][1000 genomes]
rs575719	0.81[ASN][1000 genomes]
rs575796	0.85[ASN][1000 genomes]
rs581556	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609562	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622217	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs624319	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634916	0.85[ASN][1000 genomes]
rs637614	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639426	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641990	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs668871	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs673259	0.90[ASN][1000 genomes]
rs673736	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs675162	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6905958	0.82[EUR][1000 genomes]
rs6923921	0.82[EUR][1000 genomes]
rs695174	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs884742	0.82[EUR][1000 genomes]
rs9346816	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9364552	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv886810	chr6:160700769-160897872	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv886811	chr6:160700769-161070990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv886812	chr6:160706661-161024848	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	esv3446643	chr6:160767862-160771710	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
14	esv3424011	chr6:160768387-160770935	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160768400-160770600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:160768600-160770600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr6:160768600-160770800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:160768600-160771000	Bivalent/Poised TSS	HepG2	liver
5	chr6:160768600-160771400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:160768600-160771600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:160768800-160771000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:160768800-160771200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:160768800-160771600	Active TSS	A549	lung
10	chr6:160768800-160771800	Active TSS	Aorta	Aorta
11	chr6:160769000-160770600	Active TSS	Ovary	ovary
12	chr6:160769000-160771000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:160769000-160771000	Active TSS	Rectal Smooth Muscle	rectum
14	chr6:160769000-160771400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:160769000-160771400	Active TSS	Right Atrium	heart
16	chr6:160769000-160772000	Active TSS	Psoas Muscle	Psoas
17	chr6:160769200-160770800	Active TSS	Colon Smooth Muscle	Colon
18	chr6:160769400-160770800	Bivalent/Poised TSS	Placenta	Placenta
19	chr6:160769600-160771000	Active TSS	Gastric	stomach
20	chr6:160769800-160770600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
21	chr6:160769800-160770600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr6:160769800-160770800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr6:160769800-160771000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:160769800-160771000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr6:160769800-160771200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
26	chr6:160769800-160771400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
27	chr6:160769800-160772000	Flanking Active TSS	Liver	Liver
28	chr6:160770000-160770600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:160770000-160770800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
30	chr6:160770000-160770800	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr6:160770000-160771000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr6:160770000-160771200	Enhancers	Spleen	Spleen
33	chr6:160770000-160771400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:160770000-160771400	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr6:160770000-160772000	Bivalent/Poised TSS	Lung	lung
36	chr6:160770200-160770600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:160770200-160770800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr6:160770200-160771000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:160770200-160771000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:160770400-160770600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr6:160770400-160770600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:160770400-160770600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:160770400-160770600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:160770400-160770600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:160770400-160770600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
46	chr6:160770400-160770600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:160770400-160770600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:160770400-160770600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:160770400-160770600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:160770400-160770600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

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