Variant report

Variant	rs8033067
Chromosome Location	chr15:77825495-77825496
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77824813..77828626-chr15:77832957..77835709,3	K562	blood:
2	chr15:77822210..77823977-chr15:77824433..77827126,2	MCF-7	breast:
3	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
4	chr15:77819703..77822055-chr15:77824303..77826129,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-1	chr15:77823445-77826452	ENSG00000259362.2

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10519167	0.82[JPT][hapmap]
rs11630540	0.94[ASN][1000 genomes]
rs11630557	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630916	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630926	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631274	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632602	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634174	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635567	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635606	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636529	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11639293	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898370	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12898656	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12899390	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901100	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901338	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901732	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901765	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901998	0.94[ASN][1000 genomes]
rs12902072	0.89[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs12902379	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902698	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902852	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902896	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902898	0.88[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs12902912	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12902925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902948	0.80[EUR][1000 genomes]
rs12904200	0.80[EUR][1000 genomes]
rs12904208	0.80[EUR][1000 genomes]
rs12904212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904254	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12904348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904533	0.80[EUR][1000 genomes]
rs12904584	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904709	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904823	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12905044	0.80[EUR][1000 genomes]
rs12905318	0.80[EUR][1000 genomes]
rs12909292	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910512	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910513	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910951	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12910975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911649	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12911854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911963	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914098	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914932	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915548	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916682	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12916822	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916833	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916973	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12917044	0.88[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs12917175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917431	0.80[EUR][1000 genomes]
rs17394732	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34020536	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34829483	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35284122	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35577135	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59418918	0.94[ASN][1000 genomes]
rs62007348	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62007350	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62009067	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009069	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62009071	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62009087	0.94[ASN][1000 genomes]
rs7162494	1.00[YRI][hapmap]
rs7176307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176875	0.96[ASN][1000 genomes]
rs7180732	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025968	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027056	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8032071	0.82[JPT][hapmap]
rs8032405	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033654	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040318	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8040702	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8041398	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041520	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8042307	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8033067	RP11-307C19.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77819600-77828600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:77819800-77831000	Weak transcription	Gastric	stomach
3	chr15:77820800-77826200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:77821000-77825600	Weak transcription	Fetal Brain Female	brain
5	chr15:77821000-77825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:77821000-77825800	Enhancers	Spleen	Spleen
7	chr15:77821000-77826800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:77821000-77831200	Weak transcription	Esophagus	oesophagus
9	chr15:77821400-77826000	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:77821600-77826000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:77821600-77830200	Weak transcription	Left Ventricle	heart
12	chr15:77821800-77827600	Weak transcription	Pancreas	Pancrea
13	chr15:77822000-77825600	Weak transcription	Fetal Heart	heart
14	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
15	chr15:77822400-77825600	Weak transcription	Ovary	ovary
16	chr15:77823400-77825800	Weak transcription	Fetal Intestine Large	intestine
17	chr15:77823400-77826600	Weak transcription	Fetal Intestine Small	intestine
18	chr15:77823600-77827200	Enhancers	Fetal Stomach	stomach
19	chr15:77824000-77826600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:77824200-77825600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:77824600-77825800	Weak transcription	HepG2	liver
22	chr15:77824800-77829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:77825000-77827000	Enhancers	Fetal Kidney	kidney
24	chr15:77825200-77825600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:77825200-77825800	Enhancers	Stomach Mucosa	stomach
26	chr15:77825200-77826000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:77825200-77826000	Enhancers	Brain Germinal Matrix	brain
28	chr15:77825200-77827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:77825200-77827000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr15:77825200-77827000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:77825200-77827200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr15:77825200-77827200	Enhancers	Placenta	Placenta
33	chr15:77825200-77827800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr15:77825400-77825800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:77825400-77825800	Enhancers	Right Ventricle	heart
36	chr15:77825400-77826200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr15:77825400-77826400	Enhancers	Fetal Brain Male	brain
38	chr15:77825400-77827000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:77825400-77827000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr15:77825400-77827000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr15:77825400-77827000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:77825400-77827200	Enhancers	Fetal Lung	lung
43	chr15:77825400-77827400	Enhancers	Fetal Muscle Trunk	muscle
44	chr15:77825400-77827400	Enhancers	Fetal Muscle Leg	muscle

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