Variant report

Variant	rs12904652
Chromosome Location	chr15:72548765-72548766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72521799..72524132-chr15:72546002..72548931,2	K562	blood:
2	chr15:72548498..72554612-chr15:72558312..72566000,13	MCF-7	breast:
3	chr15:72528324..72530609-chr15:72547356..72549474,2	MCF-7	breast:
4	chr15:72519778..72525226-chr15:72547384..72553620,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067225	Chromatin interaction
ENSG00000137817	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1000281	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1035744	0.89[CEU][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1037680	0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10851850	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11072346	0.87[GIH][hapmap];0.89[TSI][hapmap]
rs11072349	0.80[EUR][1000 genomes]
rs11072350	0.81[EUR][1000 genomes]
rs11072351	0.85[ASN][1000 genomes]
rs11633327	0.81[EUR][1000 genomes]
rs11634622	0.83[EUR][1000 genomes]
rs11637611	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11853101	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858015	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12442886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591313	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12591338	0.94[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592044	0.82[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap]
rs12898585	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12901886	0.82[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs12902661	0.81[ASN][1000 genomes]
rs13858	0.90[TSI][hapmap]
rs16953769	0.82[EUR][1000 genomes]
rs16956623	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16956634	0.94[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2052713	0.81[EUR][1000 genomes]
rs2607090	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2856929	0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2912231	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959930	0.81[TSI][hapmap]
rs34189331	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35112434	0.82[EUR][1000 genomes]
rs35206011	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35603965	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3743224	0.82[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs3759900	0.81[TSI][hapmap]
rs3803471	0.87[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4506844	0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4776586	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs4776589	0.83[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs4777489	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs55763892	0.85[EUR][1000 genomes]
rs62022788	0.84[EUR][1000 genomes]
rs62022789	0.83[EUR][1000 genomes]
rs6494997	0.89[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs713048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169264	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172309	0.82[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs7175792	0.83[TSI][hapmap]
rs7179427	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7179942	0.83[EUR][1000 genomes]
rs7182776	0.82[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7183196	0.94[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];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183810	0.84[EUR][1000 genomes]
rs72733369	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023703	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8027647	0.82[EUR][1000 genomes]
rs8030815	0.87[TSI][hapmap]
rs8032222	0.82[EUR][1000 genomes]
rs8038007	0.83[EUR][1000 genomes]
rs8040828	0.89[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs8192362	0.81[EUR][1000 genomes]
rs8192364	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8192386	0.94[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8192431	0.94[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12904652	SENP8	cis	cerebellum	SCAN
rs12904652	PARP6	cis	parietal	SCAN
rs12904652	TIPIN	cis	parietal	SCAN
rs12904652	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72524800-72551400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:72530400-72563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:72530800-72561200	Strong transcription	Adipose Nuclei	Adipose
4	chr15:72531000-72562400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:72531000-72563000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:72531000-72563000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:72531000-72563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:72531200-72562800	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:72531800-72561400	Strong transcription	Stomach Smooth Muscle	stomach
10	chr15:72532000-72562600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:72532200-72561000	Strong transcription	Liver	Liver
12	chr15:72532200-72561000	Strong transcription	Fetal Intestine Large	intestine
13	chr15:72532200-72561600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:72532200-72562200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:72532200-72563000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:72532400-72562600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:72532600-72562200	Strong transcription	Brain Anterior Caudate	brain
18	chr15:72532600-72562800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:72532800-72563000	Strong transcription	HSMM	muscle
20	chr15:72533000-72562000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr15:72533200-72562400	Strong transcription	Hela-S3	cervix
22	chr15:72533200-72562600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr15:72536600-72564000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:72537200-72564200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:72537600-72563400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:72538600-72561200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:72538800-72562000	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:72539000-72562200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:72539200-72549800	Strong transcription	Fetal Intestine Small	intestine
30	chr15:72539200-72550200	Strong transcription	Fetal Stomach	stomach
31	chr15:72539200-72556600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:72539200-72562200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:72539400-72553400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:72539400-72561200	Strong transcription	Left Ventricle	heart
35	chr15:72539400-72561600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:72539400-72562600	Strong transcription	Osteobl	bone
37	chr15:72539600-72561200	Strong transcription	Brain Germinal Matrix	brain
38	chr15:72539600-72562800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:72539800-72562800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:72540200-72560000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:72540200-72561400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:72540200-72561600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:72540200-72561600	Strong transcription	HSMMtube	muscle
44	chr15:72540200-72562800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:72540200-72563200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:72540400-72556600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:72540400-72560600	Strong transcription	Ovary	ovary
48	chr15:72540400-72561000	Strong transcription	Fetal Lung	lung
49	chr15:72540400-72561600	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr15:72540400-72562800	Strong transcription	A549	lung

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