Variant report

Variant	rs11074038
Chromosome Location	chr15:92606380-92606381
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	chr15:92605416..92607446-chr15:92609381..92611493,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11074040	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1158683	1.00[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12050741	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]
rs12440470	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591961	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708590	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1400786	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]
rs1543166	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1543167	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568211	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2135853	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4247079	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4340310	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4374150	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4499213	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4530111	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4644836	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4984328	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4984329	0.92[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6496890	0.86[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167618	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168605	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171310	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177406	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181950	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030627	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]
rs8039834	0.83[EUR][1000 genomes]
rs8041844	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs908650	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs908651	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs908655	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs992838	0.81[ASW][hapmap];0.89[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.99[EUR][1000 genomes];0.98[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	esv2757614	chr15:92581551-92615246	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv2760056	chr15:92581551-92615246	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	esv9948	chr15:92588543-92606763	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11074038	FANCI	cis	parietal	SCAN
rs11074038	MESP1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92591200-92610800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:92593200-92612600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:92594200-92610800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:92600800-92610200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:92603200-92610000	Weak transcription	Lung	lung
6	chr15:92603400-92611400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:92604200-92606400	Enhancers	Brain Cingulate Gyrus	brain
8	chr15:92604200-92606600	Enhancers	Right Ventricle	heart
9	chr15:92604400-92606400	Enhancers	Brain Hippocampus Middle	brain
10	chr15:92604400-92606800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr15:92604800-92606600	Enhancers	Left Ventricle	heart
12	chr15:92604800-92606600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr15:92605000-92606400	Enhancers	Aorta	Aorta
14	chr15:92605200-92607000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:92605600-92606800	Enhancers	Fetal Heart	heart
16	chr15:92605600-92610000	Weak transcription	Brain Angular Gyrus	brain
17	chr15:92605800-92610000	Weak transcription	Esophagus	oesophagus
18	chr15:92605800-92612000	Weak transcription	Spleen	Spleen
19	chr15:92605800-92612400	Weak transcription	Ovary	ovary
20	chr15:92606000-92610400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:92606000-92610800	Weak transcription	Brain Substantia Nigra	brain
22	chr15:92606200-92610000	Weak transcription	Right Atrium	heart
23	chr15:92606200-92610400	Weak transcription	Fetal Brain Male	brain
24	chr15:92606200-92611200	Weak transcription	Brain Anterior Caudate	brain

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