Variant report

Variant	rs6565236
Chromosome Location	chr16:31517648-31517649
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31513039-31517710	K562	blood:	n/a	n/a
2	POLR2A	chr16:31517320-31518128	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31517279..31520874-chr16:31722197..31727504,6	MCF-7	breast:
2	chr16:31497480..31508766-chr16:31514543..31521176,19	MCF-7	breast:
3	chr16:31516310..31522725-chr16:31722480..31728998,9	MCF-7	breast:
4	chr16:31492761..31494318-chr16:31516815..31518352,2	K562	blood:
5	chr16:31468357..31473774-chr16:31516772..31522690,14	K562	blood:
6	chr16:31463366..31472153-chr16:31517209..31524290,14	MCF-7	breast:
7	chr16:31516846..31519269-chr16:31522678..31524630,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260625	TF binding region
ENSG00000140675	Chromatin interaction
ENSG00000261474	Chromatin interaction
ENSG00000260740	Chromatin interaction
ENSG00000261731	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000197302	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11150626	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11865835	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13143	0.94[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13337037	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34081766	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3934739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519345	1.00[JPT][hapmap]
rs4889548	1.00[JPT][hapmap]
rs4889673	1.00[JPT][hapmap]
rs6565235	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6565242	1.00[JPT][hapmap]
rs7188278	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8057401	1.00[JPT][hapmap]
rs8062314	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9926717	0.94[EUR][1000 genomes]
rs9934336	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9935222	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
8	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
9	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
10	nsv1060240	chr16:31495873-31581450	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6565236	SLC5A2	cis	lung	GTEx
rs6565236	AC026471.6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31500400-31518000	Weak transcription	Small Intestine	intestine
2	chr16:31500600-31518200	Weak transcription	Stomach Mucosa	stomach
3	chr16:31501800-31518200	Weak transcription	Hela-S3	cervix
4	chr16:31502000-31518200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:31505200-31518200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr16:31508200-31518200	Weak transcription	HMEC	breast
7	chr16:31510000-31519000	Weak transcription	Aorta	Aorta
8	chr16:31510200-31518000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:31510200-31518400	Weak transcription	Fetal Kidney	kidney
10	chr16:31511200-31518600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:31511200-31518600	Weak transcription	Fetal Thymus	thymus
12	chr16:31511200-31518800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:31511400-31518200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr16:31511800-31518200	Weak transcription	A549	lung
15	chr16:31511800-31518400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr16:31512000-31518000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr16:31512000-31518000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr16:31512000-31518000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr16:31512000-31518200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr16:31512000-31518200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr16:31512000-31518200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr16:31512000-31518200	Weak transcription	NHDF-Ad	bronchial
23	chr16:31512000-31518400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr16:31512000-31518600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr16:31512000-31518600	Weak transcription	Fetal Brain Male	brain
26	chr16:31512200-31517800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:31512200-31518000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:31512200-31518200	Weak transcription	Primary T cells from cord blood	blood
29	chr16:31512200-31518200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr16:31512200-31518200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:31512200-31518200	Weak transcription	Brain Angular Gyrus	brain
32	chr16:31512200-31518400	Weak transcription	Brain Substantia Nigra	brain
33	chr16:31512200-31518400	Weak transcription	Fetal Brain Female	brain
34	chr16:31512200-31518400	Weak transcription	NH-A	brain
35	chr16:31512200-31518800	Weak transcription	Colonic Mucosa	Colon
36	chr16:31512200-31518800	Weak transcription	Esophagus	oesophagus
37	chr16:31512200-31518800	Weak transcription	Gastric	stomach
38	chr16:31512200-31518800	Weak transcription	Ovary	ovary
39	chr16:31512400-31518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr16:31512400-31518200	Weak transcription	Colon Smooth Muscle	Colon
41	chr16:31513600-31519000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr16:31513800-31518000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr16:31513800-31518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr16:31513800-31518400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr16:31513800-31518800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr16:31514000-31518200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:31514000-31518200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr16:31514000-31518400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr16:31514000-31518400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr16:31514000-31518400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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