Variant report

Variant	rs9925684
Chromosome Location	chr16:71957753-71957754
allele	C/T
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	chr16:71957631-71958299	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:71955962-71958122	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:71956027-71958896	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71955110..71958047-chr16:71963028..71965520,2	MCF-7	breast:
2	chr16:71928455..71931068-chr16:71956099..71958859,3	MCF-7	breast:

Variant related genes	Relation type
IST1	TF binding region
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000263320	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1035543	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852506	0.88[ASN][1000 genomes]
rs10852508	0.85[ASN][1000 genomes]
rs12447423	0.85[ASN][1000 genomes]
rs12600153	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12600163	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13332113	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13332180	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13337118	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1834033	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291947	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2303220	0.82[ASN][1000 genomes]
rs2878406	0.85[ASN][1000 genomes]
rs34111614	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4462592	0.85[ASN][1000 genomes]
rs4538017	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788448	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788567	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788572	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788574	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4788578	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55702379	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56309616	0.86[EUR][1000 genomes]
rs58114621	0.85[ASN][1000 genomes]
rs58609735	0.80[ASN][1000 genomes]
rs60075093	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60740701	0.91[EUR][1000 genomes]
rs7350856	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8052028	0.84[ASN][1000 genomes]
rs952159	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs952160	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889100	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921705	0.85[ASN][1000 genomes]
rs9925441	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9936965	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9937626	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71945200-71959000	Strong transcription	Primary T cells from cord blood	blood
2	chr16:71948400-71965600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr16:71948600-71964000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
4	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:71948800-71968800	Strong transcription	Dnd41	blood
7	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
8	chr16:71949000-71964600	Strong transcription	A549	lung
9	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr16:71949200-71963000	Strong transcription	K562	blood
11	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
13	chr16:71949400-71960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:71949400-71960400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr16:71949400-71963600	Strong transcription	Fetal Kidney	kidney
16	chr16:71949400-71963800	Strong transcription	Fetal Lung	lung
17	chr16:71949400-71965200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr16:71949600-71960400	Strong transcription	Placenta	Placenta
20	chr16:71949600-71964800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr16:71949800-71960000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr16:71949800-71960600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr16:71949800-71962000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr16:71949800-71963600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr16:71950000-71959600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:71950000-71964800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr16:71950200-71963400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr16:71950200-71964200	Strong transcription	Brain Germinal Matrix	brain
29	chr16:71950400-71958600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr16:71950400-71958600	Strong transcription	Hela-S3	cervix
31	chr16:71950600-71958200	Strong transcription	Lung	lung
32	chr16:71950600-71960400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr16:71950600-71961200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr16:71950600-71964800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr16:71950600-71965400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr16:71950800-71958600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr16:71950800-71958800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:71950800-71960800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr16:71950800-71960800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr16:71950800-71961000	Weak transcription	Stomach Mucosa	stomach
42	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr16:71951000-71958200	Strong transcription	Fetal Muscle Leg	muscle
44	chr16:71951000-71958600	Strong transcription	Fetal Brain Male	brain
45	chr16:71951000-71960600	Strong transcription	HepG2	liver
46	chr16:71951400-71957800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:71951400-71962000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr16:71951600-71959000	Strong transcription	Gastric	stomach
49	chr16:71951800-71958200	Strong transcription	Spleen	Spleen
50	chr16:71951800-71959800	Strong transcription	Colonic Mucosa	Colon

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