Variant report

Variant	rs9929354
Chromosome Location	chr16:70519783-70519784
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	chr16:70519715-70519786	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70510922..70516361-chr16:70517334..70521909,5	K562	blood:
2	chr16:70503488..70506383-chr16:70517357..70519879,2	MCF-7	breast:
3	chr16:70518786..70520618-chr16:70554933..70557035,2	K562	blood:

Variant related genes	Relation type
COG4	TF binding region
ENSG00000157353	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs12923937	1.00[CHD][hapmap]
rs13331220	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334577	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13334595	1.00[CHD][hapmap]
rs13339216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339561	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339593	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339643	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970226	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970240	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970243	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970253	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970259	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970260	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17878662	1.00[AMR][1000 genomes]
rs17879275	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17881316	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17881323	1.00[CHD][hapmap]
rs17881635	1.00[CHD][hapmap]
rs17883248	1.00[CHD][hapmap]
rs17883716	1.00[CHD][hapmap]
rs17885165	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17886060	1.00[CHD][hapmap]
rs17886111	1.00[AMR][1000 genomes]
rs28419202	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28438025	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28475204	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28619389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28777081	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28838669	1.00[CHD][hapmap]
rs55667445	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55885171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55926204	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56189591	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57451547	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58142695	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58144908	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59158714	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59460917	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60757048	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61641432	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6499318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184876	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7185011	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7186436	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7188297	1.00[AMR][1000 genomes]
rs7188474	1.00[AMR][1000 genomes]
rs7188808	1.00[AMR][1000 genomes]
rs7191191	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7193228	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7196773	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7199312	1.00[AMR][1000 genomes]
rs7200034	1.00[MEX][hapmap]
rs7200586	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7200978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7203007	1.00[CHD][hapmap]
rs73573163	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73573175	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578815	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8047593	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8049929	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8050767	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs8051473	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051618	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057327	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057732	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8057766	0.90[LWK][hapmap];1.00[MEX][hapmap]
rs8058754	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059200	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8061243	1.00[AMR][1000 genomes]
rs8061431	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062414	0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9302615	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921410	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921696	0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap]
rs9924352	1.00[MEX][hapmap]
rs9925510	0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs9926355	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928617	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9928808	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929882	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932065	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933022	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9936085	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9937769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9939252	0.82[AFR][1000 genomes]
rs9940353	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70501200-70535800	Strong transcription	Fetal Intestine Small	intestine
3	chr16:70501400-70535200	Strong transcription	Fetal Intestine Large	intestine
4	chr16:70501400-70536400	Strong transcription	Fetal Stomach	stomach
5	chr16:70503800-70522200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:70504200-70524800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr16:70504200-70532000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:70504400-70535200	Strong transcription	Liver	Liver
9	chr16:70506200-70524000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr16:70506400-70535200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:70506600-70522800	Weak transcription	Fetal Brain Male	brain
12	chr16:70506600-70535400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:70507000-70520400	Strong transcription	Brain Anterior Caudate	brain
14	chr16:70511000-70527400	Weak transcription	Psoas Muscle	Psoas
15	chr16:70511400-70526200	Strong transcription	Thymus	Thymus
16	chr16:70511600-70524200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr16:70511800-70524800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:70511800-70535600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:70512000-70524600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:70512000-70535400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr16:70512200-70520600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr16:70512200-70521200	Strong transcription	Fetal Thymus	thymus
23	chr16:70512800-70524200	Strong transcription	Fetal Muscle Leg	muscle
24	chr16:70512800-70533600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr16:70513000-70528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr16:70513000-70528600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr16:70513200-70522000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr16:70513600-70522600	Strong transcription	Adipose Nuclei	Adipose
30	chr16:70513600-70527600	Weak transcription	Right Atrium	heart
31	chr16:70513800-70520800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:70513800-70532200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr16:70514000-70520600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:70514000-70523400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr16:70514000-70524400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr16:70514200-70520400	Strong transcription	Lung	lung
37	chr16:70514400-70524800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr16:70514400-70527800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:70514600-70523400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr16:70514800-70524200	Weak transcription	Fetal Heart	heart
41	chr16:70515800-70524000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:70516000-70530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr16:70516200-70527200	Weak transcription	Small Intestine	intestine
44	chr16:70516600-70520400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:70516800-70521800	Strong transcription	Placenta	Placenta
46	chr16:70516800-70522200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr16:70516800-70522200	Weak transcription	Hela-S3	cervix
48	chr16:70516800-70523600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr16:70516800-70527000	Weak transcription	A549	lung
50	chr16:70516800-70527400	Weak transcription	HMEC	breast

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