Variant report

Variant	rs12445641
Chromosome Location	chr16:71967783-71967784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71958595..71960870-chr16:71966170..71968682,3	K562	blood:
2	chr16:71961957..71964879-chr16:71965668..71968577,3	K562	blood:
3	chr16:71928513..71931522-chr16:71966735..71969096,3	MCF-7	breast:
4	chr16:71958595..71960870-chr16:71966525..71968682,2	K562	blood:
5	chr16:71967092..71968643-chr16:71978130..71979874,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261337	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000263320	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10500567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852505	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10852507	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075906	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11075910	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11639843	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640135	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11648557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11861296	0.82[ASW][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs11865456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149460	0.82[JPT][hapmap]
rs12149917	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12445564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448086	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12708919	1.00[CHB][hapmap]
rs12921279	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12921459	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12927691	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928939	0.82[GIH][hapmap]
rs12934512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330178	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17357420	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17358402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288030	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2878494	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs3088285	0.85[EUR][1000 genomes]
rs34029919	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101687	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664834	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35028754	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35069141	0.81[ASN][1000 genomes]
rs35209006	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35377660	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35404791	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35535529	0.88[EUR][1000 genomes]
rs35595148	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36182990	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528577	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384782	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71386939	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71386940	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71386942	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188591	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];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7191848	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195988	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197486	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]
rs7198834	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7202840	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs73586164	0.86[ASN][1000 genomes]
rs8046044	0.85[EUR][1000 genomes]
rs8049508	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051878	1.00[CHB][hapmap]
rs8052358	0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8053906	0.84[EUR][1000 genomes]
rs8063657	0.83[EUR][1000 genomes]
rs9939911	1.00[JPT][hapmap]
rs9940234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv516948	chr16:71965725-71988728	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12445641	TMEM208	cis	parietal	SCAN
rs12445641	ZFHX3	cis	parietal	SCAN
rs12445641	TK2	cis	parietal	SCAN
rs12445641	PHLPP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71948800-71968800	Strong transcription	Dnd41	blood
2	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
3	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
4	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr16:71953200-71969600	Strong transcription	Liver	Liver
7	chr16:71953800-71969000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:71953800-71969600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:71954000-71969000	Strong transcription	GM12878-XiMat	blood
10	chr16:71954000-71969000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr16:71954000-71969400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr16:71954000-71969600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:71954200-71968200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr16:71954200-71969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr16:71955000-71969000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:71956800-71971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:71958000-71969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr16:71961800-71969600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:71962000-71971200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr16:71962400-71967800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr16:71962600-71967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:71962600-71967800	Weak transcription	Aorta	Aorta
23	chr16:71962600-71967800	Weak transcription	Pancreas	Pancrea
24	chr16:71962600-71969600	Strong transcription	Placenta	Placenta
25	chr16:71962600-71972000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:71963200-71967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr16:71963200-71967800	Weak transcription	Gastric	stomach
28	chr16:71963200-71967800	Weak transcription	Lung	lung
29	chr16:71963200-71968400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr16:71963200-71972000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr16:71963200-71972800	Weak transcription	Right Ventricle	heart
32	chr16:71963400-71968000	Weak transcription	Brain Angular Gyrus	brain
33	chr16:71963400-71969600	Strong transcription	Adipose Nuclei	Adipose
34	chr16:71963600-71967800	Weak transcription	Esophagus	oesophagus
35	chr16:71963600-71967800	Weak transcription	Left Ventricle	heart
36	chr16:71963600-71968000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr16:71963600-71968600	Weak transcription	Right Atrium	heart
38	chr16:71963600-71968800	Strong transcription	NHDF-Ad	bronchial
39	chr16:71963600-71969600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:71963600-71970200	Weak transcription	Small Intestine	intestine
41	chr16:71963600-71970800	Weak transcription	Fetal Kidney	kidney
42	chr16:71964000-71969800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr16:71964000-71970000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr16:71964000-71970000	Strong transcription	Fetal Muscle Leg	muscle
45	chr16:71964000-71971000	Weak transcription	Ovary	ovary
46	chr16:71964000-71971400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr16:71964200-71972000	Weak transcription	Psoas Muscle	Psoas
48	chr16:71964400-71969400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr16:71964400-71970000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr16:71964600-71967800	Weak transcription	Rectal Smooth Muscle	rectum

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