Variant report

Variant	rs12904384
Chromosome Location	chr15:77410878-77410879
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77316659..77317287-chr15:77410867..77411851,3	MCF-7	breast:
2	chr15:77402139..77405633-chr15:77408093..77411138,3	MCF-7	breast:
3	chr15:77410555..77412418-chr15:77788437..77789768,11	K562	blood:
4	chr15:77410739..77411823-chr15:77788848..77789944,8	MCF-7	breast:
5	chr15:77410865..77411747-chr15:77876252..77877201,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11630837	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11632999	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11637488	0.92[JPT][hapmap];0.80[TSI][hapmap]
rs11638220	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11639079	1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11639197	1.00[JPT][hapmap];0.83[TSI][hapmap]
rs12909704	1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs12910419	1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs17382798	1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs17466989	1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs33940778	0.85[JPT][hapmap]
rs4450362	0.80[ASN][1000 genomes]
rs71405237	0.80[ASN][1000 genomes]
rs7166293	0.92[JPT][hapmap]
rs7181345	0.80[ASN][1000 genomes]
rs8030500	0.80[ASN][1000 genomes]
rs8032925	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12904384	STRA6	cis	cerebellum	SCAN
rs12904384	HMG20A	cis	parietal	SCAN
rs12904384	HMG20A	cis	cerebellum	SCAN
rs12904384	SCAPER	cis	brain	BrainEAC

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77394600-77413400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr15:77397600-77411200	Weak transcription	HUVEC	blood vessel
3	chr15:77397800-77411400	Weak transcription	Fetal Thymus	thymus
4	chr15:77398000-77411600	Weak transcription	Fetal Brain Female	brain
5	chr15:77400000-77411400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:77400200-77411400	Weak transcription	Stomach Mucosa	stomach
7	chr15:77400200-77424200	Weak transcription	Esophagus	oesophagus
8	chr15:77400200-77427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:77400200-77429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:77400400-77411400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:77400400-77413000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:77400400-77428600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:77400600-77411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:77400600-77411400	Weak transcription	Brain Substantia Nigra	brain
15	chr15:77400600-77411400	Weak transcription	Small Intestine	intestine
16	chr15:77400600-77425400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:77401000-77411600	Weak transcription	Fetal Kidney	kidney
18	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
19	chr15:77401800-77411400	Weak transcription	NH-A	brain
20	chr15:77402800-77412600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:77404200-77430800	Weak transcription	Thymus	Thymus
22	chr15:77404600-77411600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:77404600-77419200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:77404600-77435600	Weak transcription	HMEC	breast
25	chr15:77405000-77411400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:77405000-77411400	Weak transcription	GM12878-XiMat	blood
27	chr15:77405200-77411400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:77406000-77411400	Weak transcription	Right Atrium	heart
29	chr15:77406400-77411400	Weak transcription	HSMMtube	muscle
30	chr15:77406600-77411400	Weak transcription	NHDF-Ad	bronchial
31	chr15:77406800-77411200	Weak transcription	Fetal Lung	lung
32	chr15:77407000-77411400	Weak transcription	HSMM	muscle
33	chr15:77407200-77411200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:77407200-77411400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:77407200-77411400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:77407200-77411400	Weak transcription	Dnd41	blood
37	chr15:77407400-77411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:77407400-77411000	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:77407400-77411200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:77407400-77411200	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:77407400-77411400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr15:77407400-77411400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:77407400-77411400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:77407400-77411400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr15:77407400-77411400	Weak transcription	Ovary	ovary
46	chr15:77407400-77411400	Weak transcription	Right Ventricle	heart
47	chr15:77407400-77411400	Weak transcription	NHLF	lung
48	chr15:77407400-77411600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:77407400-77411800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:77407400-77413000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links