Variant report

Variant	rs12631438
Chromosome Location	chr3:138154854-138154855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138153677..138156615-chr3:138182530..138184739,2	MCF-7	breast:
2	chr3:138147884..138150331-chr3:138154238..138156616,2	K562	blood:
3	chr3:138150985..138152959-chr3:138153482..138156074,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10513053	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1109088	0.96[ASN][1000 genomes]
rs11916525	0.81[JPT][hapmap]
rs12630060	0.81[JPT][hapmap]
rs12632794	0.81[JPT][hapmap]
rs12633098	0.92[ASN][1000 genomes]
rs12635904	0.81[JPT][hapmap]
rs12637679	0.81[JPT][hapmap]
rs12638938	0.95[ASN][1000 genomes]
rs13059817	0.80[JPT][hapmap]
rs13062423	0.81[JPT][hapmap]
rs13084780	0.81[JPT][hapmap]
rs13098554	0.81[JPT][hapmap]
rs1546758	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1563615	0.81[JPT][hapmap]
rs1679153	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs1679170	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1679176	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs1679177	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs1679179	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679181	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1720826	0.85[ASN][1000 genomes]
rs1720829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1720830	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs1720832	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs34963112	0.84[ASN][1000 genomes]
rs6768963	0.81[JPT][hapmap]
rs7609893	0.96[ASN][1000 genomes]
rs7611650	0.94[ASN][1000 genomes]
rs774014	0.95[ASN][1000 genomes]
rs811794	0.91[JPT][hapmap]
rs812277	0.88[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs9049	0.81[JPT][hapmap]
rs940234	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9843291	0.80[EUR][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12631438	TLX2	trans	parietal	SCAN
rs12631438	PRR23B	cis	cerebellum	SCAN
rs12631438	KRTAP19-3	trans	cerebellum	SCAN
rs12631438	TRIM42	cis	cerebellum	SCAN
rs12631438	SLC25A36	cis	cerebellum	SCAN
rs12631438	C2orf28	trans	parietal	SCAN
rs12631438	MRPS22	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138152200-138155000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:138153000-138155000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
3	chr3:138153000-138155000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
4	chr3:138153000-138155200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr3:138153200-138155000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:138153200-138155000	Active TSS	Psoas Muscle	Psoas
7	chr3:138153400-138155000	Active TSS	NHDF-Ad	bronchial
8	chr3:138153400-138155200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:138153400-138155200	Active TSS	Brain Anterior Caudate	brain
10	chr3:138153600-138155000	Active TSS	Lung	lung
11	chr3:138154200-138155000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
12	chr3:138154200-138157000	Weak transcription	HSMMtube	muscle
13	chr3:138154400-138155000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:138154400-138155000	Active TSS	Colon Smooth Muscle	Colon
15	chr3:138154400-138155000	Enhancers	Gastric	stomach
16	chr3:138154400-138155200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:138154400-138155600	Bivalent Enhancer	Fetal Heart	heart
18	chr3:138154400-138159200	Weak transcription	HepG2	liver
19	chr3:138154600-138155000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr3:138154600-138155000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr3:138154600-138155000	Bivalent Enhancer	Fetal Intestine Large	intestine
22	chr3:138154600-138155000	Bivalent Enhancer	Fetal Intestine Small	intestine
23	chr3:138154600-138155000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr3:138154600-138157600	Weak transcription	HSMM	muscle
25	chr3:138154600-138159200	Weak transcription	Right Ventricle	heart
26	chr3:138154800-138155000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr3:138154800-138155000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:138154800-138155000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:138154800-138155000	Weak transcription	Brain Angular Gyrus	brain
30	chr3:138154800-138155000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:138154800-138155000	Bivalent Enhancer	Fetal Stomach	stomach
32	chr3:138154800-138155000	Enhancers	Pancreas	Pancrea
33	chr3:138154800-138155400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr3:138154800-138160000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links