Variant report

Variant	rs12645165
Chromosome Location	chr4:106087217-106087218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106077302..106081599-chr4:106085488..106089334,5	MCF-7	breast:
2	chr4:106086235..106088556-chr4:106151811..106153985,2	MCF-7	breast:
3	chr4:106066054..106072074-chr4:106082791..106088077,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10010281	0.80[YRI][hapmap]
rs10014102	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10022109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs12641113	0.93[ASN][1000 genomes]
rs12643257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12647922	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs1391440	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17583558	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17617028	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs2189234	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2285720	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28493806	0.86[EUR][1000 genomes]
rs2903386	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs62331150	0.88[ASN][1000 genomes]
rs62331151	0.99[ASN][1000 genomes]
rs974801	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9790517	1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs9884482	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12645165	NPNT	cis	cerebellum	SCAN
rs12645165	PPA2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106087600	Weak transcription	Lung	lung
2	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
3	chr4:106069600-106102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:106069800-106101000	Weak transcription	HSMM	muscle
5	chr4:106069800-106101800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:106070400-106111600	Weak transcription	Placenta	Placenta
8	chr4:106071000-106100800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:106072600-106100600	Weak transcription	Adipose Nuclei	Adipose
10	chr4:106076200-106089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:106076200-106092800	Weak transcription	Psoas Muscle	Psoas
12	chr4:106076200-106093000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:106077000-106100800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
15	chr4:106078000-106092200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
17	chr4:106080200-106091400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:106080400-106088800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:106080400-106088800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:106080600-106101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:106080600-106102800	Weak transcription	NHEK	skin
22	chr4:106080600-106105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:106080600-106107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:106080800-106091000	Weak transcription	Ovary	ovary
25	chr4:106080800-106095200	Weak transcription	Fetal Intestine Large	intestine
26	chr4:106081000-106089400	Weak transcription	Fetal Intestine Small	intestine
27	chr4:106083400-106091400	Weak transcription	Primary T cells from cord blood	blood
28	chr4:106083600-106089200	Weak transcription	Small Intestine	intestine
29	chr4:106083600-106097200	ZNF genes & repeats	GM12878-XiMat	blood
30	chr4:106083600-106100800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:106083600-106100800	Weak transcription	Right Ventricle	heart
32	chr4:106083600-106109200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:106083800-106089000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:106083800-106089200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:106083800-106089400	Weak transcription	Fetal Brain Male	brain
36	chr4:106083800-106091400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:106083800-106092800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:106083800-106092800	Weak transcription	Brain Anterior Caudate	brain
39	chr4:106083800-106095600	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:106083800-106095800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:106083800-106100400	Weak transcription	Stomach Mucosa	stomach
42	chr4:106083800-106104800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:106083800-106111400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:106084000-106105000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:106084600-106092800	Weak transcription	K562	blood
46	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
47	chr4:106085200-106093600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:106085400-106091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:106085600-106091000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:106085600-106112800	Weak transcription	Brain Cingulate Gyrus	brain

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