Variant report

Variant	rs12050741
Chromosome Location	chr15:92579506-92579507
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92578004..92579721-chr15:92585811..92587645,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11074038	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11074040	0.85[EUR][1000 genomes]
rs1158683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12440470	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12591961	1.00[JPT][hapmap]
rs12708590	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1400786	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543166	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543167	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1568211	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2135853	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4247079	0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs4340310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4374150	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4499213	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4530111	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4644836	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4984329	0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6496890	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs7167618	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7168605	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171310	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7177406	0.80[ASN][1000 genomes]
rs7181950	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8030627	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8038377	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8039834	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041844	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs908650	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs908651	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs908655	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs992838	0.89[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv570451	chr15:92575841-92581290	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3311554	chr15:92576910-92579517	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv570456	chr15:92577382-92581290	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv570466	chr15:92577868-92580382	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12050741	FANCI	cis	parietal	SCAN
rs12050741	MESP1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92572200-92581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:92574200-92580600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:92574200-92585800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:92574800-92580600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:92574800-92585800	Weak transcription	Pancreas	Pancrea
6	chr15:92575000-92580400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:92575000-92580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:92575000-92580600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:92575400-92580400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:92575400-92580800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:92575600-92584000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:92575800-92584400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:92576000-92583800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:92576800-92580000	Weak transcription	Adipose Nuclei	Adipose
15	chr15:92576800-92580200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:92577000-92580400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:92577000-92586600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:92577200-92580200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:92577400-92580800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:92577400-92584400	Weak transcription	Brain Anterior Caudate	brain
21	chr15:92578000-92580600	Weak transcription	Aorta	Aorta
22	chr15:92578000-92583800	Weak transcription	Esophagus	oesophagus
23	chr15:92578000-92583800	Weak transcription	Right Atrium	heart
24	chr15:92578000-92584800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:92578000-92585600	Weak transcription	Spleen	Spleen
26	chr15:92578200-92583800	Weak transcription	Fetal Heart	heart
27	chr15:92578800-92581400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr15:92579000-92587000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:92579200-92583800	Weak transcription	Brain Substantia Nigra	brain
30	chr15:92579200-92583800	Weak transcription	Right Ventricle	heart
31	chr15:92579200-92585200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:92579400-92579800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:92579400-92580400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:92579400-92584400	Weak transcription	Brain Angular Gyrus	brain
35	chr15:92579400-92585200	Weak transcription	Left Ventricle	heart
36	chr15:92579400-92585200	Weak transcription	Lung	lung
37	chr15:92579400-92591200	Weak transcription	Ovary	ovary

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