Variant report

Variant	rs822739
Chromosome Location	chr1:228288218-228288219
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
2	chr1:228288054..228293498-chr1:228351743..228355627,9	K562	blood:
3	chr1:228192133..228194243-chr1:228287809..228289393,2	K562	blood:
4	chr1:228286712..228292079-chr1:228327501..228330420,5	MCF-7	breast:
5	chr1:228286985..228288771-chr1:228308857..228310947,2	K562	blood:

Variant related genes	Relation type
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143774	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs28634124	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3121310	0.88[EUR][1000 genomes]
rs6426492	0.81[ASN][1000 genomes]
rs708123	0.88[ASN][1000 genomes]
rs752107	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523917	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766972	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822725	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822733	0.80[EUR][1000 genomes]
rs822740	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs849749	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs822739	OBSCN	cis	Esophagus Mucosa	GTEx
rs822739	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
5	chr1:228279600-228289000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr1:228280200-228288800	Weak transcription	Fetal Heart	heart
7	chr1:228280800-228289600	Weak transcription	Small Intestine	intestine
8	chr1:228281400-228289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:228282400-228289200	Strong transcription	NHEK	skin
10	chr1:228282600-228288800	Strong transcription	K562	blood
11	chr1:228282600-228289000	Strong transcription	Primary T cells from cord blood	blood
12	chr1:228282800-228289000	Strong transcription	Fetal Lung	lung
13	chr1:228282800-228289200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:228282800-228289200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:228283000-228288800	Strong transcription	Dnd41	blood
16	chr1:228283000-228289000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:228283000-228289000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:228283000-228289200	Strong transcription	Brain Anterior Caudate	brain
19	chr1:228283200-228288600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:228283200-228288600	Strong transcription	Fetal Intestine Large	intestine
21	chr1:228283200-228288800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:228283200-228289200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:228283200-228289200	Genic enhancers	Gastric	stomach
24	chr1:228283400-228288600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:228283400-228288600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:228283400-228288800	Strong transcription	NHLF	lung
27	chr1:228283400-228289000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:228283400-228289200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:228283400-228289400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:228283400-228289400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:228283600-228288400	Strong transcription	Primary B cells from cord blood	blood
32	chr1:228283600-228288400	Strong transcription	HepG2	liver
33	chr1:228283600-228288800	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr1:228283600-228289000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:228283600-228289000	Strong transcription	Fetal Intestine Small	intestine
36	chr1:228283600-228289200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:228283600-228289200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:228283600-228289200	Strong transcription	Thymus	Thymus
39	chr1:228283800-228288600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:228283800-228288800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:228283800-228288800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:228283800-228289600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr1:228284000-228288600	Strong transcription	Colonic Mucosa	Colon
44	chr1:228284000-228288800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:228284000-228288800	Strong transcription	Liver	Liver
46	chr1:228284000-228289200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:228284000-228289200	Strong transcription	Fetal Thymus	thymus
48	chr1:228284000-228289400	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:228284200-228288800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:228284200-228288800	Strong transcription	Osteobl	bone

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