Variant report

Variant	rs10774577
Chromosome Location	chr12:121364324-121364325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121362910..121365338-chr12:121366492..121368266,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1067742	0.84[EUR][1000 genomes]
rs10849818	0.92[ASN][1000 genomes]
rs1105416	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065286	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1151850	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1151851	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs1151852	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1151861	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151863	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151864	0.81[ASN][1000 genomes]
rs1168945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs1696361	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696363	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718209	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1732395	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1732396	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732398	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1732405	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649994	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2649995	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2649996	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650006	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2701174	0.81[ASN][1000 genomes]
rs2701178	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2701181	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2701182	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767938	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs482522	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs487310	0.89[CHB][hapmap]
rs487912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs491602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs497273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs509152	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs532140	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs532703	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs538785	0.86[EUR][1000 genomes]
rs550349	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs551087	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs566994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs584001	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs586305	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs589699	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs594507	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs610578	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs618849	0.85[EUR][1000 genomes]
rs619679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs628771	0.87[EUR][1000 genomes]
rs631168	0.86[EUR][1000 genomes]
rs633084	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6553	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs662284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs662739	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs674021	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs679833	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs683091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs683437	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs688402	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs694303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7300722	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs791210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs791713	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv560448	chr12:121341477-121364324	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv560453	chr12:121342186-121364324	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1838192	chr12:121363589-121402932	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3421916	chr12:121364119-121367217	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10774577	P2RX4	cis	cerebellum	SCAN
rs10774577	SPPL3	cis	Adipose Subcutaneous	GTEx
rs10774577	NOS1	cis	parietal	SCAN
rs10774577	SRRM4	cis	cerebellum	SCAN
rs10774577	SPPL3	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121362800-121364400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr12:121362800-121364400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr12:121362800-121364400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:121362800-121364400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:121362800-121364400	Enhancers	Placenta	Placenta
6	chr12:121362800-121364600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:121362800-121364600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:121363000-121364400	Enhancers	Esophagus	oesophagus
9	chr12:121363000-121364400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr12:121363200-121364400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:121363200-121364400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:121363400-121364400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:121363400-121364400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:121363400-121364400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:121363400-121364400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr12:121363400-121364400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:121363400-121364400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:121363400-121364400	Enhancers	HepG2	liver
19	chr12:121363600-121364400	Enhancers	H9 Cell Line	embryonic stem cell
20	chr12:121363600-121364400	Flanking Active TSS	NHEK	skin
21	chr12:121363800-121364400	Flanking Active TSS	HMEC	breast
22	chr12:121364000-121364400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:121364000-121366600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:121364200-121364400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:121364200-121364600	ZNF genes & repeats	Fetal Thymus	thymus
26	chr12:121364200-121366800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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