Variant report

Variant	rs12898281
Chromosome Location	chr15:77786903-77786904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77780057..77783537-chr15:77786052..77789166,3	MCF-7	breast:
2	chr15:77786574..77788334-chr15:77795705..77797965,2	MCF-7	breast:
3	chr15:77779791..77781674-chr15:77785358..77787306,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10519164	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10519167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11629652	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11629835	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632602	0.88[ASN][1000 genomes]
rs11632729	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11634174	0.90[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs11636412	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639293	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11639308	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12898370	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12898656	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12899552	0.89[AFR][1000 genomes]
rs12901338	0.91[ASN][1000 genomes]
rs12902698	0.91[ASN][1000 genomes]
rs12902852	0.91[ASN][1000 genomes]
rs12902896	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12902912	0.91[ASN][1000 genomes]
rs12903253	0.85[AFR][1000 genomes]
rs12904254	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs12904823	0.81[JPT][hapmap]
rs12909645	0.82[JPT][hapmap]
rs12910951	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12911649	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12911963	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12916682	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12916973	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1554051	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16968835	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17385648	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17469276	0.91[AFR][1000 genomes]
rs17470228	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34194537	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34981488	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35235292	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35268067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35284122	0.91[ASN][1000 genomes]
rs35490414	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35902242	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55716459	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62007263	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62007348	0.91[ASN][1000 genomes]
rs62007350	0.91[ASN][1000 genomes]
rs7119	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs71407208	0.81[ASN][1000 genomes]
rs8027056	0.84[ASN][1000 genomes]
rs8032071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040318	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs8040702	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs8042307	0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12898281	STRA6	cis	cerebellum	SCAN
rs12898281	SGK269	cis	parietal	SCAN
rs12898281	HMG20A	cis	parietal	SCAN
rs12898281	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77770000-77789200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:77776200-77787600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:77776200-77788200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:77776200-77789000	Weak transcription	Colonic Mucosa	Colon
5	chr15:77776400-77788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:77776800-77788200	Weak transcription	Lung	lung
7	chr15:77777000-77788000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:77777400-77787800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:77777400-77788000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:77777400-77788000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:77777400-77788800	Weak transcription	Hela-S3	cervix
12	chr15:77777600-77787400	Weak transcription	Fetal Brain Female	brain
13	chr15:77777600-77787600	Weak transcription	Fetal Brain Male	brain
14	chr15:77777600-77787800	Weak transcription	Pancreas	Pancrea
15	chr15:77777600-77788200	Weak transcription	Brain Germinal Matrix	brain
16	chr15:77777600-77789000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:77777600-77789400	Weak transcription	Aorta	Aorta
18	chr15:77777600-77789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:77777600-77798600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:77777800-77788000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:77777800-77788000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:77777800-77788600	Weak transcription	HepG2	liver
23	chr15:77777800-77789000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:77777800-77789000	Weak transcription	A549	lung
25	chr15:77778000-77788000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:77778200-77787400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:77778200-77788200	Weak transcription	Esophagus	oesophagus
28	chr15:77779200-77788600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:77779400-77788400	Weak transcription	HMEC	breast
30	chr15:77779600-77787800	Weak transcription	Fetal Stomach	stomach
31	chr15:77779600-77788000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:77779600-77788000	Weak transcription	Brain Anterior Caudate	brain
33	chr15:77779600-77788000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:77779600-77788200	Weak transcription	Fetal Intestine Small	intestine
35	chr15:77779600-77789000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:77779800-77787800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:77779800-77787800	Weak transcription	Stomach Mucosa	stomach
38	chr15:77779800-77788200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:77780000-77787000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:77780000-77787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:77780000-77787200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:77780000-77787400	Weak transcription	Brain Substantia Nigra	brain
43	chr15:77780000-77788000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:77780000-77788000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:77780000-77788000	Weak transcription	Ovary	ovary
46	chr15:77780000-77788200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:77780000-77789000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:77780000-77789400	Weak transcription	Gastric	stomach
49	chr15:77780200-77788000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:77780200-77789000	Weak transcription	NHEK	skin

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