Variant report

Variant	rs3820475
Chromosome Location	chr1:223947605-223947606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223940335..223944037-chr1:223947483..223951720,4	K562	blood:
2	chr1:223947284..223949321-chr1:223959438..223962794,3	K562	blood:
3	chr1:223947284..223949299-chr1:223960702..223962794,2	K562	blood:
4	chr1:223938588..223941420-chr1:223947193..223949445,2	MCF-7	breast:
5	chr1:223937050..223939736-chr1:223946719..223949161,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1153943	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1153947	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1153949	0.83[EUR][1000 genomes]
rs1222146	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1222156	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1621129	0.81[AMR][1000 genomes]
rs1629850	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28370172	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4653457	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6675712	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6687003	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6694214	0.81[EUR][1000 genomes]
rs737066	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs750873	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 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	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223954400	Strong transcription	HSMM	muscle
6	chr1:223937000-223948000	Strong transcription	Lung	lung
7	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
8	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
10	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
11	chr1:223937000-223954400	Strong transcription	Gastric	stomach
12	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
17	chr1:223937000-223954800	Strong transcription	Osteobl	bone
18	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
21	chr1:223937200-223948600	Strong transcription	HUVEC	blood vessel
22	chr1:223937200-223951800	Strong transcription	HSMMtube	muscle
23	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
31	chr1:223937400-223948600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:223937400-223948600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:223937400-223951000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:223937400-223952600	Strong transcription	NH-A	brain
35	chr1:223937400-223952800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr1:223937400-223952800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:223937400-223953000	Strong transcription	Adipose Nuclei	Adipose
38	chr1:223937400-223954400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:223937400-223954400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:223937400-223954400	Strong transcription	NHLF	lung
41	chr1:223937400-223954800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:223937400-223954800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:223937400-223954800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:223937400-223954800	Strong transcription	Fetal Stomach	stomach
45	chr1:223937400-223954800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:223937400-223954800	Strong transcription	A549	lung
47	chr1:223937600-223954200	Strong transcription	Left Ventricle	heart
48	chr1:223937600-223954800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:223937800-223954800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:223937800-223954800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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