Variant report

Variant	rs12921279
Chromosome Location	chr16:71950293-71950294
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	chr16:71950166-71950535	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:71950057-71950420	K562	blood:	n/a	n/a
3	POLR2A	chr16:71950283-71950339	A549	lung:	n/a	n/a
4	POLR2A	chr16:71950138-71950865	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71949724..71951506-chr16:71954411..71956772,2	MCF-7	breast:

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

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10500567	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852507	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075906	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639843	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640135	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11644740	0.85[ASN][1000 genomes]
rs11865456	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149307	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149325	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149917	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12445564	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445641	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448086	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12921459	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12927691	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934512	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330178	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17357420	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17358402	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878494	0.86[EUR][1000 genomes]
rs3088285	0.89[EUR][1000 genomes]
rs34029919	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101687	1.00[ASN][1000 genomes]
rs34664834	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35028754	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35069141	0.81[ASN][1000 genomes]
rs35209006	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35377660	0.81[EUR][1000 genomes]
rs35404791	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35535529	0.94[EUR][1000 genomes]
rs35595148	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36182990	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751820	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528577	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384781	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384782	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71386939	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71386940	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71386942	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7185027	0.81[EUR][1000 genomes]
rs7188591	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7191848	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195988	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197486	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7198834	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73586164	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8046044	0.89[EUR][1000 genomes]
rs8049508	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050058	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052358	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8053906	0.88[EUR][1000 genomes]
rs8063657	0.87[EUR][1000 genomes]
rs9940234	0.91[EUR][1000 genomes];1.00[ASN][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	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:71932600-71951800	Weak transcription	Colonic Mucosa	Colon
4	chr16:71934400-71951000	Weak transcription	Fetal Brain Male	brain
5	chr16:71937200-71952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:71942200-71951400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr16:71942200-71951600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr16:71944000-71950400	Weak transcription	Hela-S3	cervix
9	chr16:71945200-71959000	Strong transcription	Primary T cells from cord blood	blood
10	chr16:71946000-71956000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:71948200-71952800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr16:71948400-71950800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr16:71948400-71953400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr16:71948400-71965600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr16:71948600-71952800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:71948600-71964000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr16:71948800-71950600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:71948800-71950600	Enhancers	Ovary	ovary
19	chr16:71948800-71951000	Genic enhancers	Osteobl	bone
20	chr16:71948800-71952800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr16:71948800-71953000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr16:71948800-71953200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:71948800-71968800	Strong transcription	Dnd41	blood
26	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
27	chr16:71949000-71950600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr16:71949000-71952200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr16:71949000-71952800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr16:71949000-71952800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr16:71949000-71964600	Strong transcription	A549	lung
32	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:71949200-71950800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr16:71949200-71950800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr16:71949200-71950800	Strong transcription	Thymus	Thymus
36	chr16:71949200-71951000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr16:71949200-71951000	Genic enhancers	HepG2	liver
38	chr16:71949200-71951800	Weak transcription	Fetal Heart	heart
39	chr16:71949200-71953000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr16:71949200-71953000	Weak transcription	Brain Angular Gyrus	brain
41	chr16:71949200-71954800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr16:71949200-71956000	Weak transcription	Small Intestine	intestine
43	chr16:71949200-71963000	Strong transcription	K562	blood
44	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
46	chr16:71949400-71952800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:71949400-71952800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr16:71949400-71956600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:71949400-71960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr16:71949400-71960400	Strong transcription	Rectal Mucosa Donor 29	rectum

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