Variant report

Variant	rs9925025
Chromosome Location	chr16:30644899-30644900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30553103..30555783-chr16:30644118..30646761,2	MCF-7	breast:
2	chr16:30644216..30645999-chr4:124507592..124509097,2	MCF-7	breast:
3	chr16:30440409..30443527-chr16:30644218..30646221,3	K562	blood:
4	chr16:30639009..30641962-chr16:30644620..30646873,2	MCF-7	breast:
5	chr16:30637395..30641819-chr16:30644073..30647444,4	MCF-7	breast:
6	chr16:30640142..30641957-chr16:30643713..30645899,3	K562	blood:
7	chr16:30425764..30431777-chr16:30643606..30648792,10	MCF-7	breast:
8	chr16:30437361..30442565-chr16:30644593..30648400,5	MCF-7	breast:
9	chr16:30440125..30441909-chr16:30644218..30647208,2	K562	blood:
10	chr16:30619502..30621875-chr16:30644431..30647056,2	K562	blood:
11	chr16:30643696..30645887-chr16:30676156..30678623,2	MCF-7	breast:
12	chr16:30388120..30390013-chr16:30644572..30647101,3	K562	blood:
13	chr16:30417175..30420189-chr16:30644712..30648071,3	MCF-7	breast:
14	chr16:30408965..30411877-chr16:30643615..30646400,2	MCF-7	breast:
15	chr16:30627523..30629109-chr16:30644539..30647168,2	MCF-7	breast:
16	chr16:30439875..30443880-chr16:30644269..30648773,5	MCF-7	breast:
17	chr16:30644455..30647507-chr16:30709405..30711853,4	MCF-7	breast:
18	chr16:30643767..30647614-chr16:30667017..30672688,11	MCF-7	breast:
19	chr16:30632898..30635511-chr16:30642194..30644952,2	MCF-7	breast:
20	chr16:30644081..30647716-chr16:30660195..30665578,9	MCF-7	breast:
21	chr16:30580526..30584022-chr16:30644027..30647188,4	MCF-7	breast:
22	chr16:30594953..30598897-chr16:30644540..30647635,4	MCF-7	breast:
23	chr16:30429524..30432595-chr16:30644365..30647909,3	MCF-7	breast:
24	chr16:30388287..30390366-chr16:30644424..30646542,2	MCF-7	breast:
25	chr16:30625207..30628170-chr16:30644709..30647482,2	MCF-7	breast:
26	chr16:30535592..30540399-chr16:30644319..30649503,5	K562	blood:
27	chr16:30644135..30648252-chr16:30660557..30664970,6	K562	blood:
28	chr16:30640289..30641957-chr16:30643938..30645571,2	K562	blood:
29	chr16:30644633..30647330-chr16:30647891..30651993,5	MCF-7	breast:
30	chr16:30595417..30597147-chr16:30644762..30647524,2	MCF-7	breast:
31	chr16:30614887..30616635-chr16:30644253..30647134,2	MCF-7	breast:
32	chr16:30597245..30598925-chr16:30644612..30647515,2	MCF-7	breast:
33	chr16:30644157..30647888-chr16:30708038..30710957,4	MCF-7	breast:
34	chr16:30644324..30646850-chr16:30667411..30671389,3	K562	blood:
35	chr16:30437251..30438885-chr16:30644712..30647395,2	MCF-7	breast:
36	chr16:30386731..30390013-chr16:30644584..30647173,3	K562	blood:
37	chr16:30454647..30458430-chr16:30643646..30647468,4	MCF-7	breast:
38	chr16:30644676..30647831-chr16:30651672..30654361,3	K562	blood:
39	chr16:30641739..30648234-chr16:30659002..30664628,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000156853	Chromatin interaction
ENSG00000179965	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000229809	Chromatin interaction
ENSG00000260167	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000197162	Chromatin interaction
ENSG00000260113	Chromatin interaction
ENSG00000260678	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000199787	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000239791	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12918327	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13338946	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs1348039	0.82[YRI][hapmap]
rs1470129	0.82[YRI][hapmap]
rs1530201	0.82[YRI][hapmap]
rs2289442	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs28728333	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28841118	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919428	0.91[YRI][hapmap]
rs34699226	0.91[ASN][1000 genomes]
rs35629860	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs35661204	0.85[ASN][1000 genomes]
rs36063822	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs36064568	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747481	0.94[CHD][hapmap];0.85[GIH][hapmap]
rs3747486	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs3812999	1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs4485386	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889490	1.00[CHD][hapmap]
rs4889502	0.82[YRI][hapmap]
rs4889506	0.82[YRI][hapmap]
rs55875685	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6565195	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6565196	0.87[EUR][1000 genomes]
rs67693285	1.00[ASN][1000 genomes]
rs7184055	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7185620	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186852	0.83[ASW][hapmap];0.96[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187359	1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap]
rs7187802	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7188789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7188927	0.82[YRI][hapmap]
rs7191389	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191761	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198250	1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs7204632	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7499339	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7500719	0.82[CHD][hapmap];0.85[GIH][hapmap]
rs8046001	0.88[CHD][hapmap]
rs8058578	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs8058961	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs885107	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs893924	0.82[YRI][hapmap]
rs893925	0.82[YRI][hapmap]
rs9927137	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
7	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
8	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
9	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9925025	PHKG2	cis	parietal	SCAN
rs9925025	BCL7C	cis	cerebellum	SCAN
rs9925025	C16orf93	cis	parietal	SCAN
rs9925025	ZNF768	cis	parietal	SCAN
rs9925025	YPEL3	cis	cerebellum	SCAN
rs9925025	DCTPP1	cis	cerebellum	SCAN
rs9925025	MYST1	cis	parietal	SCAN
rs9925025	MYST1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30638200-30645000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr16:30640200-30645000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr16:30640200-30645000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr16:30640200-30645000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:30640200-30645000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr16:30640200-30645000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:30640200-30645000	Weak transcription	Adipose Nuclei	Adipose
8	chr16:30640200-30645000	Weak transcription	Colonic Mucosa	Colon
9	chr16:30640200-30645000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr16:30640200-30645000	Weak transcription	Fetal Brain Male	brain
11	chr16:30640200-30645000	Weak transcription	Fetal Intestine Small	intestine
12	chr16:30640200-30645000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr16:30640200-30645000	Weak transcription	Placenta	Placenta
14	chr16:30640200-30645000	Weak transcription	Fetal Stomach	stomach
15	chr16:30640200-30645000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:30640200-30645000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr16:30640200-30645000	Weak transcription	Right Atrium	heart
18	chr16:30640200-30645000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr16:30640400-30645000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr16:30640400-30645000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr16:30640400-30645000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr16:30640400-30645000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr16:30640600-30645000	Weak transcription	Primary T cells from cord blood	blood
24	chr16:30640600-30645000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr16:30640600-30645000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr16:30640600-30645000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:30640600-30645000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr16:30640600-30645000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr16:30640600-30645000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr16:30640600-30645000	Weak transcription	Brain Anterior Caudate	brain
31	chr16:30640600-30645000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr16:30640600-30645000	Weak transcription	GM12878-XiMat	blood
33	chr16:30640600-30645000	Weak transcription	Hela-S3	cervix
34	chr16:30642000-30645000	Weak transcription	HepG2	liver
35	chr16:30644000-30645000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr16:30644600-30645000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr16:30644600-30645200	Flanking Active TSS	Dnd41	blood
38	chr16:30644800-30645000	Enhancers	Primary B cells from cord blood	blood
39	chr16:30644800-30645000	Enhancers	Primary B cells from peripheral blood	blood
40	chr16:30644800-30645000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr16:30644800-30645000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:30644800-30645000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:30644800-30645000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr16:30644800-30645000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr16:30644800-30645000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr16:30644800-30645000	Enhancers	Fetal Muscle Leg	muscle
47	chr16:30644800-30645000	Enhancers	Fetal Thymus	thymus
48	chr16:30644800-30645000	Enhancers	Thymus	Thymus
49	chr16:30644800-30645000	Flanking Active TSS	K562	blood
50	chr16:30644800-30645200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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