Variant report

Variant	rs3820543
Chromosome Location	chr1:150812858-150812859
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150788780..150790984-chr1:150810777..150813008,2	MCF-7	breast:
2	chr1:150807087..150808986-chr1:150811625..150814317,2	MCF-7	breast:
3	chr1:150803170..150805446-chr1:150810913..150813203,2	K562	blood:
4	chr1:150800531..150803502-chr1:150811550..150815655,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10788795	0.91[EUR][1000 genomes]
rs10888396	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204700	0.82[EUR][1000 genomes]
rs11204714	0.88[EUR][1000 genomes]
rs11204715	0.88[EUR][1000 genomes]
rs11204727	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11576175	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12728254	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16840074	0.85[EUR][1000 genomes]
rs1811698	0.82[ASN][1000 genomes]
rs1932864	0.82[EUR][1000 genomes]
rs2134688	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738483	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820541	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4379678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs533928	0.88[EUR][1000 genomes]
rs61817598	0.85[EUR][1000 genomes]
rs61817599	0.82[EUR][1000 genomes]
rs61817600	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61817649	0.88[EUR][1000 genomes]
rs6661100	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6671703	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679701	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6684611	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6688248	0.88[EUR][1000 genomes]
rs6692277	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6696167	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72704624	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7517566	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520511	0.80[EUR][1000 genomes]
rs7520516	0.80[EUR][1000 genomes]
rs7529204	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535848	0.88[EUR][1000 genomes]
rs7535975	0.88[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	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1010875	chr1:150796816-150845827	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	esv1793983	chr1:150804748-150825924	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv1797905	chr1:150811005-150813057	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150782200-150813000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:150783200-150816600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:150783200-150816800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:150792200-150814800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:150792600-150815400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:150793000-150816400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:150793200-150823200	Strong transcription	Placenta	Placenta
8	chr1:150793600-150815800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:150793800-150813800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:150794000-150813600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:150797000-150814400	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:150797400-150813000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:150797400-150813400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:150797600-150813400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr1:150797600-150815600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:150798200-150815600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:150799600-150816600	Strong transcription	HSMM	muscle
18	chr1:150799800-150817800	Strong transcription	Primary B cells from cord blood	blood
19	chr1:150801800-150814800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:150801800-150818600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:150801800-150824600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:150802800-150815200	Strong transcription	Fetal Lung	lung
23	chr1:150803200-150813200	Strong transcription	Colon Smooth Muscle	Colon
24	chr1:150805800-150824600	Weak transcription	HMEC	breast
25	chr1:150807200-150814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:150807200-150820800	Weak transcription	Spleen	Spleen
27	chr1:150807400-150824600	Weak transcription	A549	lung
28	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
29	chr1:150808000-150821600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
31	chr1:150809000-150813000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:150809000-150816400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:150809000-150819200	Weak transcription	K562	blood
34	chr1:150809000-150823000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:150809000-150824400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:150809000-150824600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:150809200-150814200	Weak transcription	Stomach Mucosa	stomach
38	chr1:150809200-150820600	Weak transcription	Brain Germinal Matrix	brain
39	chr1:150809200-150824600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:150809400-150813800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:150809400-150815000	Strong transcription	Liver	Liver
43	chr1:150809400-150821000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:150809400-150821000	Weak transcription	Thymus	Thymus
45	chr1:150809400-150823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:150809600-150813000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:150809600-150820400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
49	chr1:150809800-150814000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:150810000-150824800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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