Variant report

Variant	rs12447090
Chromosome Location	chr16:70516109-70516110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70510287..70517781-chr16:70555054..70559513,7	MCF-7	breast:
2	chr16:70507845..70510277-chr16:70513994..70516516,2	K562	blood:
3	chr16:70412596..70415415-chr16:70513984..70516318,3	MCF-7	breast:
4	chr16:70510715..70512361-chr16:70515275..70517741,2	MCF-7	breast:
5	chr16:70515238..70517748-chr16:70555099..70558723,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189091	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000157353	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11075767	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs11075770	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs1134074	1.00[ASW][hapmap]
rs11641683	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs11643373	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs11645437	0.86[JPT][hapmap]
rs11645585	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11648402	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs11866400	0.82[JPT][hapmap]
rs12597401	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12925729	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2168606	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2288491	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2303792	0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2303793	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs34087264	0.83[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs3762171	0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs3852695	0.87[CEU][hapmap]
rs3859068	0.90[JPT][hapmap]
rs4284632	0.91[JPT][hapmap]
rs4436771	0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs4513092	0.91[JPT][hapmap]
rs4985525	1.00[ASW][hapmap]
rs6499320	0.91[JPT][hapmap]
rs7189474	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs7192268	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs7192865	0.85[TSI][hapmap]
rs7200430	0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs7201750	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7204583	0.91[JPT][hapmap]
rs722579	0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs744672	0.86[ASN][1000 genomes]
rs7919	0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs8049641	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs8051506	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs8052125	0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs8053436	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs8057610	0.90[CHD][hapmap];0.91[JPT][hapmap]
rs8058224	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs8062178	0.91[JPT][hapmap]
rs8062183	0.86[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs8063990	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs8064013	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs936994	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs9934440	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs9936225	0.88[CHD][hapmap];0.91[JPT][hapmap]

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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12447090	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs12447090	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs12447090	RANBP10	cis	parietal	SCAN
rs12447090	TMCO7	cis	parietal	SCAN
rs12447090	CLEC18C	cis	Whole Blood	GTEx
rs12447090	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs12447090	PDPR	cis	cerebellum	SCAN
rs12447090	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs12447090	CLEC18A	cis	Artery Aorta	GTEx
rs12447090	EXOSC6	cis	parietal	SCAN
rs12447090	WWP2	cis	parietal	SCAN
rs12447090	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12447090	CLEC18A	cis	Whole Blood	GTEx
rs12447090	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs12447090	CLEC18C	cis	lung	GTEx
rs12447090	EXOSC6	cis	cerebellum	SCAN

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	chr16:70495000-70519000	Strong transcription	Primary T cells from cord blood	blood
3	chr16:70501200-70535800	Strong transcription	Fetal Intestine Small	intestine
4	chr16:70501400-70535200	Strong transcription	Fetal Intestine Large	intestine
5	chr16:70501400-70536400	Strong transcription	Fetal Stomach	stomach
6	chr16:70503800-70522200	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr16:70504200-70524800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr16:70504200-70532000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:70504400-70535200	Strong transcription	Liver	Liver
10	chr16:70506000-70518200	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr16:70506200-70518800	Strong transcription	Brain Cingulate Gyrus	brain
12	chr16:70506200-70524000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr16:70506400-70517400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr16:70506400-70535200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr16:70506600-70522800	Weak transcription	Fetal Brain Male	brain
16	chr16:70506600-70535400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr16:70506800-70518000	Strong transcription	Pancreas	Pancrea
18	chr16:70507000-70518800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr16:70507000-70518800	Strong transcription	Fetal Brain Female	brain
20	chr16:70507000-70520400	Strong transcription	Brain Anterior Caudate	brain
21	chr16:70510600-70519000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr16:70510800-70518800	Strong transcription	Primary B cells from cord blood	blood
23	chr16:70511000-70527400	Weak transcription	Psoas Muscle	Psoas
24	chr16:70511400-70526200	Strong transcription	Thymus	Thymus
25	chr16:70511600-70524200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:70511800-70516800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:70511800-70518400	Strong transcription	Gastric	stomach
28	chr16:70511800-70518800	Strong transcription	Dnd41	blood
29	chr16:70511800-70524800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:70511800-70535600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:70512000-70518000	Strong transcription	Brain Substantia Nigra	brain
32	chr16:70512000-70518200	Strong transcription	Rectal Smooth Muscle	rectum
33	chr16:70512000-70518800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:70512000-70518800	Strong transcription	Ovary	ovary
35	chr16:70512000-70519000	Strong transcription	Brain Germinal Matrix	brain
36	chr16:70512000-70524600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr16:70512000-70535400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr16:70512200-70516800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr16:70512200-70516800	Genic enhancers	NHEK	skin
40	chr16:70512200-70518000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr16:70512200-70518000	Strong transcription	Aorta	Aorta
42	chr16:70512200-70518800	Strong transcription	Brain Angular Gyrus	brain
43	chr16:70512200-70520600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr16:70512200-70521200	Strong transcription	Fetal Thymus	thymus
45	chr16:70512400-70516400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr16:70512400-70516800	Strong transcription	GM12878-XiMat	blood
47	chr16:70512600-70518800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr16:70512800-70516200	Strong transcription	A549	lung
49	chr16:70512800-70518800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:70512800-70524200	Strong transcription	Fetal Muscle Leg	muscle

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