Variant report

Variant	rs7197486
Chromosome Location	chr16:71958052-71958053
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	chr16:71957832-71958172	HepG2	liver:	n/a	n/a
2	GATA3	chr16:71957781-71958796	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr16:71957631-71958299	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:71955962-71958122	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:71956027-71958896	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10500567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10852505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs10852507	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11075906	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11075909	0.87[YRI][hapmap]
rs11075910	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11639843	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11640135	0.92[EUR][1000 genomes]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11648557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11861296	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11865456	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12149307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12149325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12149460	0.82[JPT][hapmap]
rs12149917	0.93[EUR][1000 genomes]
rs12445564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12445641	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12448086	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12708919	1.00[CHB][hapmap]
rs12921279	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12921459	0.93[EUR][1000 genomes]
rs12927691	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12928939	0.82[GIH][hapmap]
rs12934512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13330178	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17357420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17358402	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288030	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2878494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3088285	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34029919	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34101687	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34664834	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35028754	0.92[EUR][1000 genomes]
rs35209006	0.91[EUR][1000 genomes]
rs35377660	0.86[EUR][1000 genomes]
rs35404791	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35535529	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35595148	0.89[EUR][1000 genomes]
rs36182990	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3751820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788568	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4788575	0.85[JPT][hapmap]
rs4788579	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs71384781	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384782	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71386939	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71386940	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71386942	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7185027	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7187418	0.87[YRI][hapmap]
rs7188591	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7191848	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7195988	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7198834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7202840	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs73586164	0.84[EUR][1000 genomes]
rs8046044	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8049508	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8050058	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8051878	1.00[CHB][hapmap]
rs8052358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8053906	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8054602	0.87[YRI][hapmap]
rs8063657	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9939404	0.87[YRI][hapmap]
rs9939911	1.00[JPT][hapmap]
rs9940234	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7197486	TMEM208	cis	parietal	SCAN
rs7197486	PHLPP2	cis	cerebellum	SCAN
rs7197486	TK2	cis	parietal	SCAN
rs7197486	PHLPP2	cis	lymphoblastoid	seeQTL

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	chr16:71951400-71962000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr16:71951600-71959000	Strong transcription	Gastric	stomach
48	chr16:71951800-71958200	Strong transcription	Spleen	Spleen
49	chr16:71951800-71959800	Strong transcription	Colonic Mucosa	Colon
50	chr16:71951800-71960600	Strong transcription	Brain Cingulate Gyrus	brain

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