Variant report

Variant	rs4336916
Chromosome Location	chr1:212590678-212590679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
2	chr1:212526286..212528256-chr1:212589016..212590996,2	K562	blood:
3	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
4	chr1:212589362..212592084-chr1:212630605..212632407,2	K562	blood:

Variant related genes	Relation type
ENSG00000117691	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11803766	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12739715	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12755383	0.99[EUR][1000 genomes]
rs17018997	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35702733	1.00[EUR][1000 genomes]
rs35822123	0.82[EUR][1000 genomes]
rs4540733	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6666415	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6669027	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6676208	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6693849	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6697910	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6704234	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71646158	0.82[EUR][1000 genomes]
rs71646159	0.93[EUR][1000 genomes]
rs71646161	0.99[EUR][1000 genomes]
rs7533689	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7551910	0.99[EUR][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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4336916	RP11-15I11.3	cis	Thyroid	GTEx
rs4336916	RP11-15I11.3	cis	lung	GTEx
rs4336916	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212588600-212595000	Weak transcription	Right Atrium	heart
2	chr1:212588800-212590800	Enhancers	Brain Angular Gyrus	brain
3	chr1:212588800-212591800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:212589000-212591000	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:212589000-212591000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr1:212589000-212591400	Enhancers	Brain Substantia Nigra	brain
7	chr1:212589000-212591800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:212589000-212592600	Enhancers	K562	blood
9	chr1:212589200-212591600	Weak transcription	Spleen	Spleen
10	chr1:212589200-212593600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:212589200-212593800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:212589400-212591800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:212589400-212591800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:212589400-212593800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:212590000-212594200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:212590400-212591200	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:212590400-212592000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:212590600-212590800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:212590600-212590800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:212590600-212590800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:212590600-212590800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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