Variant report

Variant	rs12902898
Chromosome Location	chr15:77849191-77849192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77847726..77850177-chr15:77859392..77861698,2	K562	blood:
2	chr15:77848566..77850112-chr15:77856631..77859198,2	K562	blood:
3	chr15:77848268..77851249-chr15:77883793..77885346,2	MCF-7	breast:
4	chr15:77840852..77845440-chr15:77846808..77850692,5	K562	blood:
5	chr15:77848438..77851266-chr15:77854844..77857960,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259420	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11634174	0.88[CEU][hapmap]
rs11635226	0.85[EUR][1000 genomes]
rs11636231	0.85[EUR][1000 genomes]
rs11637932	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11639293	0.88[CEU][hapmap]
rs12898370	0.88[CEU][hapmap]
rs12898656	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12901471	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap]
rs12901732	0.82[CEU][hapmap];0.92[CHB][hapmap]
rs12902072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902698	0.82[CEU][hapmap]
rs12902896	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12902925	1.00[JPT][hapmap]
rs12902948	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904200	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904208	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904212	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12904348	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12904533	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904823	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12905044	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905318	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909292	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]
rs12909645	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs12909808	0.88[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs12910594	0.88[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs12910951	0.88[CEU][hapmap]
rs12910975	0.88[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs12911649	0.88[CEU][hapmap]
rs12911854	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs12911963	0.88[CEU][hapmap]
rs12912386	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs12913005	0.85[EUR][1000 genomes]
rs12914932	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12915057	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916515	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap]
rs12916642	0.88[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs12916682	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12916973	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12917044	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917175	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs12917314	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap]
rs12917431	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17394732	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2667781	0.81[EUR][1000 genomes]
rs2667782	0.81[EUR][1000 genomes]
rs2667783	0.81[EUR][1000 genomes]
rs2682927	0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs34075648	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34607443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34829483	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35577135	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35657172	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55883527	0.85[EUR][1000 genomes]
rs7176307	0.88[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs7180732	0.86[EUR][1000 genomes]
rs7181283	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs8025968	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8032405	0.80[EUR][1000 genomes]
rs8033067	0.80[EUR][1000 genomes]
rs8040318	0.88[CEU][hapmap]
rs8040702	0.88[CEU][hapmap]
rs8041398	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8041520	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8042307	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12902898	STRA6	cis	cerebellum	SCAN
rs12902898	C15orf5	cis	parietal	SCAN
rs12902898	HMG20A	cis	cerebellum	SCAN
rs12902898	SGK269	cis	parietal	SCAN
rs12902898	RP11-307C19.1	cis	Heart Left Ventricle	GTEx
rs12902898	ABCB8	trans	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77838600-77849800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:77841600-77849600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:77842200-77850200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr15:77842800-77850400	Enhancers	Brain Hippocampus Middle	brain
5	chr15:77844400-77850200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:77844600-77850000	Enhancers	Brain Anterior Caudate	brain
7	chr15:77844800-77849800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:77844800-77849800	Enhancers	Brain Substantia Nigra	brain
9	chr15:77845000-77849400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:77846200-77850200	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:77846800-77850000	Enhancers	Fetal Lung	lung
12	chr15:77847000-77851200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:77847400-77850800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:77847600-77849200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:77847600-77850000	Weak transcription	Spleen	Spleen
16	chr15:77847800-77849600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:77847800-77849600	Weak transcription	Left Ventricle	heart
18	chr15:77848000-77849800	Enhancers	Brain Germinal Matrix	brain
19	chr15:77848000-77855800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:77848200-77849400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:77848400-77849200	Enhancers	Fetal Brain Male	brain
22	chr15:77848400-77849600	Enhancers	Fetal Intestine Small	intestine
23	chr15:77848600-77849800	Enhancers	Fetal Brain Female	brain
24	chr15:77848600-77850000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:77848600-77850000	Enhancers	Brain Angular Gyrus	brain
26	chr15:77848600-77850200	Enhancers	Fetal Intestine Large	intestine
27	chr15:77848600-77850600	Enhancers	Placenta	Placenta
28	chr15:77848800-77849400	Enhancers	Fetal Muscle Leg	muscle
29	chr15:77848800-77850200	Enhancers	Fetal Heart	heart
30	chr15:77848800-77850400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr15:77849000-77849600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:77849000-77850200	Enhancers	H1 Cell Line	embryonic stem cell
33	chr15:77849000-77850200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr15:77849000-77850200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr15:77849000-77850200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:77849000-77850200	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links