Variant report

Variant	rs12909292
Chromosome Location	chr15:77837982-77837983
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77837272..77839702-chr15:77860514..77863715,3	MCF-7	breast:
2	chr15:77837146..77840341-chr15:77840841..77844639,4	K562	blood:
3	chr15:77818777..77820332-chr15:77836618..77838168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259420	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11630540	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11630557	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630916	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630926	0.89[ASN][1000 genomes]
rs11631274	0.91[ASN][1000 genomes]
rs11634174	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs11635226	0.82[EUR][1000 genomes]
rs11635567	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11635606	0.89[ASN][1000 genomes]
rs11636231	0.82[EUR][1000 genomes]
rs11636529	0.91[ASN][1000 genomes]
rs11637932	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11639293	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs12898370	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs12898656	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[TSI][hapmap]
rs12899390	0.91[ASN][1000 genomes]
rs12901100	0.90[ASN][1000 genomes]
rs12901471	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs12901732	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12901765	0.91[ASN][1000 genomes]
rs12901998	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12902072	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12902379	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902698	0.82[CEU][hapmap]
rs12902896	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[TSI][hapmap]
rs12902898	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12902925	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12902948	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904200	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904208	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904212	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904254	0.86[JPT][hapmap]
rs12904348	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904533	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904584	0.91[ASN][1000 genomes]
rs12904709	0.91[ASN][1000 genomes]
rs12904823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905044	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12905318	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12909645	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12909808	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910512	0.91[ASN][1000 genomes]
rs12910513	0.91[ASN][1000 genomes]
rs12910594	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12910951	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap]
rs12910975	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12911649	0.88[CEU][hapmap]
rs12911854	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12911963	0.88[CEU][hapmap]
rs12912386	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12913005	0.82[EUR][1000 genomes]
rs12914098	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915057	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12915548	0.91[ASN][1000 genomes]
rs12916515	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs12916642	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12916682	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[TSI][hapmap]
rs12916822	0.91[ASN][1000 genomes]
rs12916833	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12916973	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[TSI][hapmap]
rs12917044	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12917175	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs12917314	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12917431	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17394732	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34020536	0.89[ASN][1000 genomes]
rs34075648	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34607443	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34829483	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35577135	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657172	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55883527	0.82[EUR][1000 genomes]
rs59418918	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62009067	0.89[ASN][1000 genomes]
rs62009069	0.91[ASN][1000 genomes]
rs62009071	0.87[ASN][1000 genomes]
rs62009087	0.97[ASN][1000 genomes]
rs7176307	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7176875	0.96[ASN][1000 genomes]
rs7180732	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181283	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs8025968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032405	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033067	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033654	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8040318	0.88[CEU][hapmap];0.86[CHD][hapmap]
rs8040702	0.88[CEU][hapmap]
rs8041398	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041520	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042307	0.88[CEU][hapmap];0.86[CHD][hapmap]

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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking 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	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS 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	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12909292	ABCB8	trans	parietal	SCAN
rs12909292	SGK269	cis	parietal	SCAN
rs12909292	STRA6	cis	cerebellum	SCAN
rs12909292	RP11-307C19.1	cis	Heart Left Ventricle	GTEx
rs12909292	HMG20A	cis	cerebellum	SCAN
rs12909292	C15orf5	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
2	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77833800-77843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:77834000-77841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:77834200-77840800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:77835800-77838000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:77835800-77838200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:77836200-77838000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:77836200-77838000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:77836200-77838000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:77836200-77838000	Weak transcription	Left Ventricle	heart
12	chr15:77836200-77838000	Weak transcription	A549	lung
13	chr15:77836200-77838000	Weak transcription	HMEC	breast
14	chr15:77836200-77838000	Weak transcription	NH-A	brain
15	chr15:77836200-77838000	Weak transcription	NHDF-Ad	bronchial
16	chr15:77836200-77838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:77836200-77838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:77836200-77838200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:77836200-77838200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:77836200-77838200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:77836200-77838200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:77836200-77838200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:77836200-77838200	Weak transcription	Adipose Nuclei	Adipose
24	chr15:77836200-77838400	Weak transcription	HUVEC	blood vessel
25	chr15:77836200-77839000	Enhancers	Stomach Mucosa	stomach
26	chr15:77836200-77839600	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:77836200-77840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:77836200-77841000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:77836200-77841000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:77836200-77841000	Weak transcription	Fetal Thymus	thymus
31	chr15:77836200-77841200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:77836200-77841200	Weak transcription	K562	blood
33	chr15:77836200-77841400	Weak transcription	Brain Anterior Caudate	brain
34	chr15:77836200-77846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:77836400-77838000	Weak transcription	Hela-S3	cervix
36	chr15:77836400-77838200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:77836400-77838400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:77836400-77838400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:77836400-77838400	Weak transcription	GM12878-XiMat	blood
40	chr15:77836600-77838400	Weak transcription	Fetal Stomach	stomach
41	chr15:77836800-77838000	Weak transcription	Placenta	Placenta
42	chr15:77836800-77838000	Weak transcription	Right Atrium	heart
43	chr15:77836800-77838000	Weak transcription	Right Ventricle	heart
44	chr15:77836800-77838000	Weak transcription	Spleen	Spleen
45	chr15:77836800-77838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:77837000-77840400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:77837600-77838800	Enhancers	Gastric	stomach
48	chr15:77837600-77839000	Enhancers	NHLF	lung
49	chr15:77837800-77838000	Enhancers	Lung	lung
50	chr15:77837800-77839000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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