Variant report

Variant	rs2236361
Chromosome Location	chr1:227935280-227935281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227934449-227938226	PBDE	blood:	n/a	n/a
2	POLR2A	chr1:227935224-227935401	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
2	chr1:227916288..227917792-chr1:227932623..227935322,2	K562	blood:
3	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:

Variant related genes	Relation type
SNAP47	TF binding region
SNAP47-AS1	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1056699	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1060295	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799430	0.86[EUR][1000 genomes]
rs10799439	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916188	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916191	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916203	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1111046	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1155807	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1810680	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1923823	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2104245	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2236360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4500311	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6426468	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6426473	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6660432	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6693054	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6703846	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs730684	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522634	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7526184	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533588	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534403	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7536765	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7539282	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552193	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9786978	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9969994	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227923800-227935600	Weak transcription	Aorta	Aorta
2	chr1:227924000-227935400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227924000-227935600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:227924000-227936400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:227924200-227935400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:227924200-227935400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:227924200-227935400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:227924200-227935400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:227924200-227935400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:227924200-227935400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:227924200-227935400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:227924200-227935400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:227924200-227935600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:227924200-227935600	Weak transcription	Primary B cells from cord blood	blood
15	chr1:227924200-227935800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:227924200-227935800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:227924200-227935800	Weak transcription	A549	lung
18	chr1:227924200-227936000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:227924200-227936000	Weak transcription	Fetal Kidney	kidney
20	chr1:227924200-227940800	Weak transcription	HSMMtube	muscle
21	chr1:227924200-227941200	Weak transcription	HSMM	muscle
22	chr1:227924200-227941200	Weak transcription	NHDF-Ad	bronchial
23	chr1:227924200-227941600	Weak transcription	Osteobl	bone
24	chr1:227924200-227942000	Weak transcription	Hela-S3	cervix
25	chr1:227924200-227946800	Weak transcription	HUVEC	blood vessel
26	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:227924400-227935400	Weak transcription	Fetal Lung	lung
28	chr1:227924400-227935800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:227924400-227936200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:227924600-227935400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:227924800-227935400	Weak transcription	Brain Substantia Nigra	brain
32	chr1:227924800-227935600	Weak transcription	Colonic Mucosa	Colon
33	chr1:227924800-227941400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:227925000-227935400	Weak transcription	Adipose Nuclei	Adipose
35	chr1:227925000-227935400	Weak transcription	K562	blood
36	chr1:227925000-227935600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:227925000-227936000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:227925000-227941400	Weak transcription	Fetal Brain Male	brain
39	chr1:227925200-227935400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:227925200-227935600	Weak transcription	HepG2	liver
41	chr1:227925200-227941200	Weak transcription	Psoas Muscle	Psoas
42	chr1:227925400-227935600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:227925600-227935800	Weak transcription	GM12878-XiMat	blood
44	chr1:227925600-227941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227928200-227935400	Weak transcription	Brain Angular Gyrus	brain
46	chr1:227928600-227941200	Weak transcription	Small Intestine	intestine
47	chr1:227929200-227935800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:227929600-227935400	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:227930200-227945600	Weak transcription	NH-A	brain
50	chr1:227930400-227939400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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