Variant report

Variant	rs4965260
Chromosome Location	chr15:100157136-100157137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100142017..100143605-chr15:100156751..100158277,2	MCF-7	breast:
2	chr15:100148518..100150039-chr15:100155372..100157267,2	MCF-7	breast:
3	chr15:100151549..100153058-chr15:100155251..100157136,2	MCF-7	breast:
4	chr15:100156211..100158384-chr15:100167394..100168954,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10468175	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11247112	0.84[AMR][1000 genomes]
rs11247116	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631947	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs12324876	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12438623	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12441033	0.80[AMR][1000 genomes]
rs12442313	0.84[ASW][hapmap];0.89[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs12591308	0.84[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap]
rs1991921	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012129	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs325400	0.84[JPT][hapmap]
rs4564541	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes]
rs62040140	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62040141	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62040142	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7162940	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7172418	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]
rs7173943	0.86[MKK][hapmap]
rs7181542	1.00[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8029326	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8037206	0.93[CHB][hapmap];0.88[CHD][hapmap];0.81[TSI][hapmap]

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	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
2	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
3	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
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4965260	LYSMD4	cis	cerebellum	SCAN
rs4965260	LYSMD4	cis	parietal	SCAN
rs4965260	MEF2A	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100133000-100159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:100133000-100159200	Weak transcription	A549	lung
3	chr15:100141000-100157200	Weak transcription	Fetal Kidney	kidney
4	chr15:100142600-100159200	Weak transcription	Gastric	stomach
5	chr15:100142800-100159200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:100142800-100159400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr15:100142800-100164000	Weak transcription	Fetal Thymus	thymus
8	chr15:100142800-100176400	Weak transcription	Fetal Stomach	stomach
9	chr15:100143000-100163200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:100143800-100159200	Weak transcription	Lung	lung
11	chr15:100144000-100159200	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:100144000-100180800	Weak transcription	Thymus	Thymus
13	chr15:100145600-100159200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:100146200-100159200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:100148600-100159200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:100150800-100159200	Weak transcription	HSMM	muscle
17	chr15:100153000-100158600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:100153200-100160400	Enhancers	Liver	Liver
19	chr15:100153400-100159000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:100153400-100159400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:100154000-100157200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:100154000-100158200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr15:100154000-100159600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:100154800-100158000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:100155000-100159400	Weak transcription	Hela-S3	cervix
26	chr15:100155200-100157200	Weak transcription	NHDF-Ad	bronchial
27	chr15:100155200-100158200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr15:100155200-100159200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:100155200-100159200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:100155200-100159200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:100155200-100159200	Weak transcription	Colonic Mucosa	Colon
32	chr15:100155200-100159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:100155200-100159200	Weak transcription	Pancreas	Pancrea
34	chr15:100155200-100159200	Weak transcription	NHLF	lung
35	chr15:100155200-100160600	Enhancers	Fetal Heart	heart
36	chr15:100155200-100163600	Weak transcription	Dnd41	blood
37	chr15:100155200-100191000	Weak transcription	HSMMtube	muscle
38	chr15:100155400-100158200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:100155400-100158400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:100155400-100158400	Weak transcription	Osteobl	bone
41	chr15:100155400-100158800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:100155400-100158800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:100155400-100159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:100155400-100159200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:100155400-100159200	Weak transcription	Esophagus	oesophagus
46	chr15:100155400-100159200	Weak transcription	Placenta	Placenta
47	chr15:100155400-100159400	Weak transcription	Small Intestine	intestine
48	chr15:100155400-100164200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:100155400-100168400	Weak transcription	Stomach Mucosa	stomach
50	chr15:100155400-100170800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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