Variant report

Variant	rs12902379
Chromosome Location	chr15:77827968-77827969
allele	C/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	chr15:77800050..77802176-chr15:77827673..77829514,2	MCF-7	breast:
3	chr15:77827126..77831240-chr15:77834209..77836612,4	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11630540	0.89[ASN][1000 genomes]
rs11630557	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630916	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630926	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11631274	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11635567	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11635606	0.84[ASN][1000 genomes]
rs11636529	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11639293	0.81[AMR][1000 genomes]
rs12898370	0.81[AMR][1000 genomes]
rs12898656	0.80[AMR][1000 genomes]
rs12899390	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12901100	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12901471	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901732	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901765	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901998	0.89[ASN][1000 genomes]
rs12902698	0.81[AMR][1000 genomes]
rs12902852	0.81[AMR][1000 genomes]
rs12902912	0.80[AMR][1000 genomes]
rs12902925	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904212	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904348	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904584	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904709	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12904823	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12909292	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12909645	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12909808	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910512	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910513	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910594	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910975	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12911854	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912386	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12914098	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12914932	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915548	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916515	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916642	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916682	0.80[AMR][1000 genomes]
rs12916822	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916833	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916973	0.80[AMR][1000 genomes]
rs12917175	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12917314	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17394732	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34020536	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34829483	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35577135	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59418918	0.89[ASN][1000 genomes]
rs62009067	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62009069	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62009071	0.83[ASN][1000 genomes]
rs62009087	0.89[ASN][1000 genomes]
rs7176307	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176875	0.91[ASN][1000 genomes]
rs7180732	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181283	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8025968	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027056	0.81[AMR][1000 genomes]
rs8032405	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8033067	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8033654	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8041398	0.87[ASN][1000 genomes]
rs8041520	0.87[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
rs12902379	RP11-307C19.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr15:77821000-77831200	Weak transcription	Esophagus	oesophagus
4	chr15:77821600-77830200	Weak transcription	Left Ventricle	heart
5	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
6	chr15:77824800-77829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:77825800-77828600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:77825800-77828600	Weak transcription	Brain Substantia Nigra	brain
9	chr15:77825800-77830200	Weak transcription	Right Ventricle	heart
10	chr15:77825800-77831000	Weak transcription	Stomach Mucosa	stomach
11	chr15:77826400-77829800	Weak transcription	Fetal Brain Male	brain
12	chr15:77826600-77829200	Weak transcription	Fetal Brain Female	brain
13	chr15:77826800-77828400	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:77826800-77828600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:77826800-77828600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:77826800-77828600	Weak transcription	Brain Angular Gyrus	brain
17	chr15:77827000-77828200	Weak transcription	Fetal Intestine Small	intestine
18	chr15:77827000-77828400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:77827000-77828400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:77827000-77828400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:77827000-77828400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:77827000-77828400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:77827000-77828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:77827000-77828400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:77827000-77828400	Weak transcription	Brain Anterior Caudate	brain
26	chr15:77827000-77828400	Weak transcription	Fetal Intestine Large	intestine
27	chr15:77827000-77828600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:77827000-77828600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:77827000-77828600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:77827000-77828600	Weak transcription	Brain Germinal Matrix	brain
31	chr15:77827000-77828800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:77827000-77829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:77827000-77829600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:77827000-77829800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:77827000-77833200	Weak transcription	HSMMtube	muscle
36	chr15:77827000-77835400	Weak transcription	Psoas Muscle	Psoas
37	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
38	chr15:77827200-77828400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:77827200-77828400	Weak transcription	Fetal Lung	lung
40	chr15:77827200-77828400	Weak transcription	Placenta	Placenta
41	chr15:77827200-77828600	Weak transcription	Fetal Heart	heart
42	chr15:77827200-77828600	Weak transcription	Fetal Stomach	stomach
43	chr15:77827200-77830200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:77827400-77828400	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:77827400-77828400	Weak transcription	Spleen	Spleen
46	chr15:77827400-77829400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:77827600-77828600	Weak transcription	HepG2	liver
48	chr15:77827600-77832400	Enhancers	Pancreas	Pancrea
49	chr15:77827600-77834000	Enhancers	Primary B cells from peripheral blood	blood
50	chr15:77827800-77830000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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