Variant report

Variant	rs1400786
Chromosome Location	chr15:92586139-92586140
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:92495196..92498509-chr15:92585959..92588143,4	MCF-7	breast:
2	chr15:92578004..92579721-chr15:92585811..92587645,2	K562	blood:
3	chr15:92584947..92586453-chr15:92587413..92590025,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11074038	1.00[CEU][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11074040	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1158683	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050741	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]
rs12440470	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591961	0.94[JPT][hapmap]
rs12708590	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1543166	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543167	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1568211	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2135853	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4247079	0.97[CHD][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs4340310	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4374150	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4499213	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4530111	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4644836	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4984328	0.81[ASN][1000 genomes]
rs4984329	0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs6496890	0.86[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs7167618	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168605	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7171310	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7177406	0.82[ASN][1000 genomes]
rs7181950	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8030627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038377	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8039834	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041844	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs908650	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs908651	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs908655	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs992838	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.97[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:5 , 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	esv2757614	chr15:92581551-92615246	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2760056	chr15:92581551-92615246	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1668	chr15:92585344-92635991	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1400786	FANCI	cis	parietal	SCAN
rs1400786	MESP1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92577000-92586600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:92579000-92587000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:92579400-92591200	Weak transcription	Ovary	ovary
4	chr15:92581000-92593400	Weak transcription	Aorta	Aorta
5	chr15:92581200-92586600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:92581400-92586800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:92583800-92586400	Enhancers	Brain Substantia Nigra	brain
8	chr15:92583800-92587200	Enhancers	Fetal Heart	heart
9	chr15:92583800-92587400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr15:92583800-92588200	Enhancers	Right Atrium	heart
11	chr15:92584000-92586200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr15:92584000-92588000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:92584400-92586200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:92584400-92586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:92584400-92587200	Weak transcription	Right Ventricle	heart
16	chr15:92584600-92586200	Enhancers	Brain Cingulate Gyrus	brain
17	chr15:92584600-92586600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:92584600-92587400	Weak transcription	Psoas Muscle	Psoas
19	chr15:92584600-92592600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:92584800-92587000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:92585200-92587400	Enhancers	Lung	lung
22	chr15:92585200-92588200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:92585200-92588200	Enhancers	Left Ventricle	heart
24	chr15:92585400-92601200	Weak transcription	Fetal Brain Male	brain
25	chr15:92585600-92586200	Enhancers	Spleen	Spleen
26	chr15:92585600-92587600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:92585600-92591400	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:92585800-92586200	Enhancers	Pancreas	Pancrea
29	chr15:92585800-92587800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:92585800-92588200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:92585800-92592600	Weak transcription	Brain Anterior Caudate	brain
32	chr15:92586000-92587000	Weak transcription	Esophagus	oesophagus
33	chr15:92586000-92587200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:92586000-92588000	Enhancers	NHEK	skin
35	chr15:92586000-92591000	Weak transcription	Brain Angular Gyrus	brain
36	chr15:92586000-92593200	Weak transcription	Gastric	stomach

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