Variant report

Variant	rs191256
Chromosome Location	chr15:100248220-100248221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100105316..100107211-chr15:100246606..100248832,2	MCF-7	breast:
2	chr15:100247213..100249293-chr15:100253745..100255884,2	K562	blood:
3	chr15:100104091..100109623-chr15:100241901..100248412,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1019974	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs11247119	0.93[CEU][hapmap];0.81[CHD][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12592092	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12593522	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs12593785	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12595285	0.87[EUR][1000 genomes]
rs12901291	0.93[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912791	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs12916000	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1434232	0.82[JPT][hapmap]
rs167805	0.93[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs170521	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs170522	0.90[CEU][hapmap];0.89[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs188977	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2033546	0.87[CEU][hapmap];0.81[CHD][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2117309	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2570808	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs2570816	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2570825	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2581467	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2581468	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2581470	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2581472	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2862869	0.82[EUR][1000 genomes]
rs2862870	0.84[EUR][1000 genomes]
rs2902349	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325381	0.82[JPT][hapmap]
rs325390	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs325392	0.87[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs325394	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs325404	0.93[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs325409	0.93[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs325410	0.93[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs325413	0.87[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34443706	0.84[EUR][1000 genomes]
rs35410986	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35441914	0.84[EUR][1000 genomes]
rs3730281	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4424892	0.82[JPT][hapmap]
rs4965532	0.83[EUR][1000 genomes]
rs7162392	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7165899	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs73482408	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7496677	0.87[CEU][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs892465	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs897073	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
11	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv1045838	chr15:100243067-101032218	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv904564	chr15:100245296-100723798	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs191256	LYSMD4	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100248800	Weak transcription	Gastric	stomach
3	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:100219600-100248400	Weak transcription	Spleen	Spleen
5	chr15:100231000-100250600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:100233400-100248400	Weak transcription	Right Ventricle	heart
7	chr15:100233400-100248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:100233400-100248800	Weak transcription	Esophagus	oesophagus
9	chr15:100233400-100248800	Weak transcription	Fetal Intestine Small	intestine
10	chr15:100233400-100248800	Weak transcription	Lung	lung
11	chr15:100233400-100248800	Weak transcription	Ovary	ovary
12	chr15:100233400-100248800	Weak transcription	Pancreas	Pancrea
13	chr15:100233400-100250600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:100233400-100250800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:100233400-100251200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:100233600-100248800	Weak transcription	Fetal Brain Male	brain
17	chr15:100233800-100250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:100233800-100256600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:100234800-100248400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:100235000-100248800	Weak transcription	Colonic Mucosa	Colon
21	chr15:100235200-100250800	Weak transcription	Brain Germinal Matrix	brain
22	chr15:100236600-100250800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:100236800-100249200	Weak transcription	Placenta	Placenta
24	chr15:100237000-100250000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:100237200-100250200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:100241800-100248800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:100244400-100250200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:100244400-100250800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:100244600-100248400	Weak transcription	Hela-S3	cervix
30	chr15:100244600-100248400	Weak transcription	HepG2	liver
31	chr15:100244600-100248600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:100244600-100248600	Weak transcription	A549	lung
33	chr15:100244600-100248800	Weak transcription	K562	blood
34	chr15:100244600-100249400	Weak transcription	Fetal Intestine Large	intestine
35	chr15:100244600-100250000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:100244600-100250600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:100244600-100250800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:100244600-100250800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:100244600-100250800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:100244600-100252800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr15:100244600-100254800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:100244600-100272400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:100244800-100250800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:100245000-100251600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:100245000-100258200	Weak transcription	Fetal Kidney	kidney
46	chr15:100245600-100256200	Strong transcription	Dnd41	blood
47	chr15:100245600-100258000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:100246200-100248400	Genic enhancers	GM12878-XiMat	blood
49	chr15:100246200-100257000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:100246400-100248400	Enhancers	Thymus	Thymus

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