Variant report

Variant	rs4788450
Chromosome Location	chr16:71955400-71955401
allele	G/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:5)
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	chr16:71954530-71955697	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:71954131-71955741	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71955110..71958047-chr16:71963028..71965520,2	MCF-7	breast:
2	chr16:71955313..71957451-chr16:71962491..71964232,2	K562	blood:
3	chr16:71949724..71951506-chr16:71954411..71956772,2	MCF-7	breast:
4	chr16:71925187..71928062-chr16:71954742..71956995,2	MCF-7	breast:
5	chr16:71927590..71930855-chr16:71952254..71956665,4	MCF-7	breast:

No data

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

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11075908	0.92[YRI][hapmap]
rs11075910	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs12444594	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12444829	0.82[AFR][1000 genomes]
rs12708918	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12708919	0.96[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12928939	1.00[CHB][hapmap]
rs17286411	0.82[ASW][hapmap]
rs1834036	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288030	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs2288031	0.88[YRI][hapmap]
rs35619990	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788449	0.92[YRI][hapmap]
rs4788561	0.85[EUR][1000 genomes]
rs4788566	0.86[YRI][hapmap]
rs4788568	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4788569	0.88[EUR][1000 genomes]
rs4788575	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs4788579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7184486	0.85[YRI][hapmap]
rs8044004	0.85[EUR][1000 genomes]
rs8044335	0.85[EUR][1000 genomes]
rs8050651	0.88[YRI][hapmap]
rs8059053	0.82[AFR][1000 genomes]
rs8063324	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs9932707	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4788450	TMEM208	cis	parietal	SCAN
rs4788450	MTSS1L	cis	parietal	SCAN
rs4788450	HP,HPR	cis	brain	BrainEAC
rs4788450	PDXDC2P	cis	cerebellum	SCAN
rs4788450	HPR	cis	cerebellum	SCAN
rs4788450	AARS	cis	parietal	SCAN
rs4788450	PSMD7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:71945200-71959000	Strong transcription	Primary T cells from cord blood	blood
3	chr16:71946000-71956000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:71948400-71965600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr16:71948600-71964000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
6	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr16:71948800-71968800	Strong transcription	Dnd41	blood
9	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
10	chr16:71949000-71964600	Strong transcription	A549	lung
11	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:71949200-71956000	Weak transcription	Small Intestine	intestine
13	chr16:71949200-71963000	Strong transcription	K562	blood
14	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
16	chr16:71949400-71956600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr16:71949400-71960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr16:71949400-71960400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr16:71949400-71963600	Strong transcription	Fetal Kidney	kidney
20	chr16:71949400-71963800	Strong transcription	Fetal Lung	lung
21	chr16:71949400-71965200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:71949600-71960400	Strong transcription	Placenta	Placenta
24	chr16:71949600-71964800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr16:71949800-71960000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr16:71949800-71960600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:71949800-71962000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:71949800-71963600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr16:71950000-71959600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:71950000-71964800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:71950200-71963400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr16:71950200-71964200	Strong transcription	Brain Germinal Matrix	brain
33	chr16:71950400-71958600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr16:71950400-71958600	Strong transcription	Hela-S3	cervix
35	chr16:71950600-71958200	Strong transcription	Lung	lung
36	chr16:71950600-71960400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr16:71950600-71961200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr16:71950600-71964800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr16:71950600-71965400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:71950800-71958600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:71950800-71958800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr16:71950800-71960800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr16:71950800-71960800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr16:71950800-71961000	Weak transcription	Stomach Mucosa	stomach
46	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr16:71951000-71958200	Strong transcription	Fetal Muscle Leg	muscle
48	chr16:71951000-71958600	Strong transcription	Fetal Brain Male	brain
49	chr16:71951000-71960600	Strong transcription	HepG2	liver
50	chr16:71951400-71957800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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