Variant report

Variant	rs2012129
Chromosome Location	chr15:100132917-100132918
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	chr15:100108232..100110845-chr15:100132819..100134406,2	K562	blood:
2	chr15:100105039..100107202-chr15:100131797..100134740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11247112	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11247116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631947	0.84[ASW][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap]
rs12324876	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438623	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs12441033	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12442313	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591308	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs1991921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs325405	0.82[ASN][1000 genomes]
rs4564541	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs4965260	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]
rs60381510	0.86[ASN][1000 genomes]
rs62040140	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62040141	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7162940	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172418	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]
rs7173943	0.87[CHB][hapmap];0.83[MKK][hapmap]
rs7181542	0.84[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029326	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs8037206	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2012129	LYSMD4	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100107400-100134200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100107400-100134200	Weak transcription	Pancreas	Pancrea
3	chr15:100108000-100142000	Weak transcription	Thymus	Thymus
4	chr15:100109000-100140200	Weak transcription	Hela-S3	cervix
5	chr15:100115000-100138800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:100118800-100139800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:100120400-100134200	Weak transcription	Aorta	Aorta
8	chr15:100120800-100140200	Weak transcription	HSMM	muscle
9	chr15:100120800-100142600	Weak transcription	Ovary	ovary
10	chr15:100122000-100136400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:100123200-100136800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:100124600-100142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:100126600-100134200	Weak transcription	Brain Angular Gyrus	brain
14	chr15:100126800-100136800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:100127000-100139200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:100128200-100142400	Weak transcription	Placenta	Placenta
17	chr15:100128600-100135800	Weak transcription	Small Intestine	intestine
18	chr15:100128800-100137400	Weak transcription	Fetal Thymus	thymus
19	chr15:100129400-100141800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:100129400-100142400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:100129400-100155200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:100129800-100133000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr15:100130000-100133200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr15:100130000-100153000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:100130400-100133600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr15:100130600-100137200	ZNF genes & repeats	GM12878-XiMat	blood
27	chr15:100131200-100133000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:100131200-100133000	Enhancers	Right Ventricle	heart
29	chr15:100131200-100133000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr15:100131200-100133400	Enhancers	NHDF-Ad	bronchial
31	chr15:100131200-100133600	Enhancers	Liver	Liver
32	chr15:100131200-100137000	Enhancers	Fetal Heart	heart
33	chr15:100131400-100133200	Weak transcription	Primary B cells from cord blood	blood
34	chr15:100131400-100142600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:100131600-100134200	Enhancers	Colon Smooth Muscle	Colon
36	chr15:100131800-100133200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:100131800-100140000	Weak transcription	Fetal Intestine Large	intestine
38	chr15:100132000-100134200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:100132000-100140200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:100132200-100133000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:100132200-100133000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:100132200-100133000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:100132200-100133000	Enhancers	NHEK	skin
44	chr15:100132200-100133000	Enhancers	Osteobl	bone
45	chr15:100132200-100133200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:100132200-100133200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr15:100132200-100133200	Enhancers	Stomach Mucosa	stomach
48	chr15:100132200-100133200	Enhancers	HUVEC	blood vessel
49	chr15:100132200-100133600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:100132200-100133600	Enhancers	Sigmoid Colon	Sigmoid Colon

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