Variant report

Variant	rs4247079
Chromosome Location	chr15:92615785-92615786
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	chr15:92613588..92616911-chr15:92617353..92620743,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11074038	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]
rs11074040	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1158683	0.94[CHD][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap]
rs12050741	0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs12440470	0.86[ASN][1000 genomes]
rs12591961	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12708590	0.86[ASN][1000 genomes]
rs1400786	0.97[CHD][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs1568211	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2135853	0.86[ASN][1000 genomes]
rs4340310	0.86[ASW][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap]
rs4374150	0.84[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4530111	0.87[ASN][1000 genomes]
rs4644836	0.92[CHB][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4984328	0.87[ASN][1000 genomes]
rs4984329	0.92[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.84[ASN][1000 genomes]
rs6496890	0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs7171310	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7177406	0.87[ASN][1000 genomes]
rs7181950	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs8030627	0.97[CHD][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs8041844	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs908650	0.84[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs908651	0.84[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs908655	0.85[ASN][1000 genomes]
rs992838	0.85[ASW][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4247079	MESP1	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92609800-92616000	Enhancers	Brain Cingulate Gyrus	brain
2	chr15:92610800-92620400	Enhancers	Brain Substantia Nigra	brain
3	chr15:92612200-92616200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:92612800-92617400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:92613000-92617600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:92613000-92617800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:92613000-92620600	Weak transcription	Pancreas	Pancrea
8	chr15:92613200-92617600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:92613400-92616200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:92613400-92616400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:92613400-92616400	Weak transcription	Small Intestine	intestine
12	chr15:92613400-92616600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:92613400-92616800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:92613400-92617600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr15:92613400-92617600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:92613400-92617600	Weak transcription	NHLF	lung
17	chr15:92613400-92617800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:92613400-92618000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:92613400-92618000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:92613400-92621000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:92613600-92615800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:92613600-92616200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:92613600-92616400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:92613600-92617400	Weak transcription	Osteobl	bone
25	chr15:92613600-92617600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:92613600-92617600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:92613600-92617600	Weak transcription	A549	lung
28	chr15:92613600-92617600	Weak transcription	HMEC	breast
29	chr15:92613600-92617600	Weak transcription	HUVEC	blood vessel
30	chr15:92613600-92620000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:92613600-92628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:92613800-92615800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:92613800-92617400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:92613800-92617600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr15:92613800-92617600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:92614000-92616400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:92614000-92616800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:92614200-92616400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:92614200-92621000	Enhancers	Fetal Heart	heart
40	chr15:92614200-92621200	Enhancers	Brain Hippocampus Middle	brain
41	chr15:92614400-92617400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:92614400-92621000	Enhancers	Lung	lung
43	chr15:92614600-92617400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:92614600-92617400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:92614600-92617400	Weak transcription	NHEK	skin
46	chr15:92614600-92617600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:92614600-92617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:92614600-92617800	Weak transcription	Liver	Liver
49	chr15:92614600-92626600	Weak transcription	Psoas Muscle	Psoas
50	chr15:92614800-92616400	Enhancers	Stomach Mucosa	stomach

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