Variant report

Variant	rs7172418
Chromosome Location	chr15:100143418-100143419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:100142017..100143605-chr15:100156751..100158277,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10468175	0.81[AMR][1000 genomes]
rs11247112	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11247116	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631947	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs12324876	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12438623	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs12441033	0.81[AMR][1000 genomes]
rs12442313	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12591308	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs1991921	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2012129	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs325405	0.85[ASN][1000 genomes]
rs4564541	1.00[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4965260	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60381510	0.81[ASN][1000 genomes]
rs62040140	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62040141	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62040142	0.84[AMR][1000 genomes]
rs7162940	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173943	0.87[CHB][hapmap]
rs7178948	0.83[GIH][hapmap]
rs7181542	0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029326	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs8037206	0.88[ASW][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][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	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv904558	chr15:100019382-100171684	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv1798883	chr15:100124483-100153969	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7172418	MEF2A	cis	cerebellum	SCAN
rs7172418	LYSMD4	cis	parietal	SCAN
rs7172418	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100129400-100155200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:100130000-100153000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:100132600-100154800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:100132800-100153200	Weak transcription	HepG2	liver
5	chr15:100133000-100143600	Weak transcription	Brain Anterior Caudate	brain
6	chr15:100133000-100144400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:100133000-100145400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:100133000-100145600	Weak transcription	NH-A	brain
9	chr15:100133000-100153400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:100133000-100155000	Weak transcription	Esophagus	oesophagus
11	chr15:100133000-100157000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:100133000-100159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:100133000-100159200	Weak transcription	A549	lung
14	chr15:100133200-100144200	Weak transcription	HUVEC	blood vessel
15	chr15:100133200-100148000	Weak transcription	Stomach Mucosa	stomach
16	chr15:100133800-100143600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:100133800-100146000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:100135000-100149200	Weak transcription	Pancreas	Pancrea
19	chr15:100135400-100145000	Weak transcription	Aorta	Aorta
20	chr15:100135600-100152000	Weak transcription	HSMMtube	muscle
21	chr15:100135800-100153600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:100137800-100143800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:100138200-100143800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:100138400-100145400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:100138800-100143600	ZNF genes & repeats	GM12878-XiMat	blood
26	chr15:100138800-100149200	Weak transcription	Fetal Brain Male	brain
27	chr15:100139000-100153800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr15:100140000-100153400	Weak transcription	Fetal Intestine Small	intestine
29	chr15:100140200-100145000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:100140600-100145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:100140600-100147200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:100140800-100144800	Weak transcription	NHEK	skin
33	chr15:100140800-100148000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:100140800-100148000	Weak transcription	Fetal Brain Female	brain
35	chr15:100140800-100153400	Weak transcription	Fetal Intestine Large	intestine
36	chr15:100141000-100144000	Weak transcription	Osteobl	bone
37	chr15:100141000-100147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:100141000-100148000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:100141000-100150800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:100141000-100152600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:100141000-100154800	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:100141000-100156600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:100141000-100156800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:100141000-100157200	Weak transcription	Fetal Kidney	kidney
45	chr15:100141200-100150400	Weak transcription	HSMM	muscle
46	chr15:100141200-100152800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:100141200-100154000	Weak transcription	Hela-S3	cervix
48	chr15:100141200-100154000	Weak transcription	NHDF-Ad	bronchial
49	chr15:100141600-100148600	Enhancers	Fetal Heart	heart
50	chr15:100141800-100145000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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