Variant report

Variant	rs2912231
Chromosome Location	chr15:72567957-72567958
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:72567956-72568006	GM12878	blood:	n/a
2	chr15:72567956-72568006	PANC-1	pancreas:	n/a
3	chr15:72567956-72568006	HRE	kidney:	n/a
4	chr15:72567956-72568006	HepG2	liver:	n/a
5	chr15:72567956-72568006	AG09319	gingival:	n/a
6	chr15:72567956-72568006	HCPEpiC	choroid plexus:	n/a
7	chr15:72567956-72568006	CMK	blood:	n/a
8	chr15:72567956-72568006	RPTEC	kidney:	n/a
9	chr15:72567956-72568006	HCM	heart:	n/a
10	chr15:72567956-72568006	SK-N-MC	brain:	n/a
11	chr15:72567956-72568006	HCF	heart:	n/a
12	chr15:72567956-72568006	IMR90	lung:	fetal
13	chr15:72567956-72568006	NHDF-neo	bronchial:	n/a
14	chr15:72567956-72568006	AG09309	skin:	n/a
15	chr15:72567956-72568006	PFSK-1	brain:	n/a
16	chr15:72567956-72568006	BJ	skin:	n/a
17	chr15:72567956-72568006	HRPEpiC	eye:	n/a
18	chr15:72567956-72568006	SAEC	small airway:	n/a
19	chr15:72567956-72568006	K562	blood:	n/a
20	chr15:72567956-72568006	SK-N-SH_RA	brain:	n/a
21	chr15:72567956-72568006	ECC-1	luminal epithelium:	n/a
22	chr15:72567956-72568006	HMEC	breast:	n/a
23	chr15:72567956-72568006	Hepatocyte	liver:	n/a
24	chr15:72567956-72568006	H1-hESC	embryonic stem cell:	embryo
25	chr15:72567956-72568006	HEK293	kidney:	embryo
26	chr15:72567956-72568006	MCF-7	breast:	n/a
27	chr15:72567956-72568006	ovcar-3	ovarian:	n/a
28	chr15:72567956-72568006	HNPCEpiC	eye:	n/a
29	chr15:72567956-72568006	U87	brain:	n/a
30	chr15:72567956-72568006	AoSMC	blood vessel:	n/a
31	chr15:72567956-72568006	Caco-2	colon:	n/a
32	chr15:72567956-72568006	HAEpiC	amniotic membrane:	n/a
33	chr15:72567956-72568006	HPAEpiC	pulmonary alveolar:	n/a
34	chr15:72567956-72568006	PrEC	prostate:	n/a
35	chr15:72567956-72568006	NB4	blood:	n/a
36	chr15:72567956-72568006	GM19239	blood:	n/a
37	chr15:72567956-72568006	GM12892	blood:	n/a
38	chr15:72567956-72568006	NT2-D1	testis:	n/a
39	chr15:72567956-72568006	HRCEpiC	kidney:	n/a
40	chr15:72567956-72568006	NH-A	brain:	n/a
41	chr15:72567956-72568006	T-47D	breast:	n/a
42	chr15:72567956-72568006	BE2_C	brain:	n/a
43	chr15:72567956-72568006	A549	lung:	n/a
44	chr15:72567956-72568006	SKMC	muscle:	n/a
45	chr15:72567956-72568006	NHBE	bronchial:	n/a
46	chr15:72567956-72568006	HCT-116	colon:	n/a
47	chr15:72567956-72568006	HL-60	blood:	n/a
48	chr15:72567956-72568006	Hela-S3	cervix:	n/a
49	chr15:72567956-72568006	GM06990	blood:	n/a
50	chr15:72567956-72568006	AG04450	lung:	fetal

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72514333..72526693-chr15:72558323..72568559,52	MCF-7	breast:
2	chr15:72519310..72525410-chr15:72562881..72568730,22	MCF-7	breast:
3	chr15:72518424..72531344-chr15:72562525..72571046,23	K562	blood:
4	chr15:72513653..72518363-chr15:72563063..72568184,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261460	CpG island
PARP6	CpG island
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1000281	0.83[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1035744	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs1037680	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851850	0.83[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs11072346	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs11072351	0.92[ASN][1000 genomes]
rs11637611	0.83[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs11853101	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858015	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442886	0.94[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs12591313	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591338	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591426	0.82[EUR][1000 genomes]
rs12592044	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12898585	0.80[EUR][1000 genomes]
rs12901886	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs12902661	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12904652	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]
rs12908882	0.80[ASN][1000 genomes]
rs13858	0.82[TSI][hapmap]
rs16953769	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16956634	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2034879	0.80[TSI][hapmap]
rs2607090	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856929	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2959930	0.89[TSI][hapmap]
rs34487006	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35112434	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35206011	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35713471	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3743224	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759900	0.89[TSI][hapmap]
rs3803471	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4238449	0.85[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4506844	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs4776586	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4776589	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4777489	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs55854204	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60921026	0.82[ASN][1000 genomes]
rs6494997	0.83[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs713048	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7169264	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7172309	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap]
rs7182776	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7183196	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72733369	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8023703	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8030815	0.80[TSI][hapmap]
rs8040828	0.83[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs8192364	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8192386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8192431	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1601	chr15:72549885-72585176	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv3366898	chr15:72567548-72569446	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2912231	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs2912231	SENP8	cis	cerebellum	SCAN
rs2912231	PARP6	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72565600-72569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:72565800-72568400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:72565800-72572600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:72566000-72568600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:72566000-72568800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:72566000-72571000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:72566000-72573600	Weak transcription	Brain Anterior Caudate	brain
8	chr15:72566000-72573600	Weak transcription	Brain Substantia Nigra	brain
9	chr15:72566000-72575800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:72566000-72576400	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:72566000-72577800	Weak transcription	Fetal Intestine Small	intestine
12	chr15:72566000-72582400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:72566000-72611400	Weak transcription	Right Ventricle	heart
14	chr15:72566200-72573000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:72566200-72573600	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:72566200-72577000	Weak transcription	Ovary	ovary
17	chr15:72566200-72577600	Weak transcription	Brain Angular Gyrus	brain
18	chr15:72566200-72578400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:72566200-72579200	Weak transcription	Primary T cells from cord blood	blood
20	chr15:72566400-72573600	Weak transcription	K562	blood
21	chr15:72567000-72611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:72567400-72569000	Enhancers	HSMMtube	muscle
23	chr15:72567600-72569200	Enhancers	HSMM	muscle
24	chr15:72567800-72568800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr15:72567800-72581400	Weak transcription	Fetal Muscle Leg	muscle

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