Variant report

Variant	rs1679168
Chromosome Location	chr3:138192192-138192193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138185730..138189738-chr3:138190908..138194397,4	MCF-7	breast:
2	chr3:138186886..138189284-chr3:138191772..138193552,2	K562	blood:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1082037	0.86[ASN][1000 genomes]
rs1088055	0.86[ASN][1000 genomes]
rs1091528	0.82[CEU][hapmap]
rs10935284	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709290	0.90[TSI][hapmap]
rs13101081	1.00[ASN][1000 genomes]
rs1379257	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1479930	1.00[ASN][1000 genomes]
rs1600511	1.00[ASN][1000 genomes]
rs1630766	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1673593	0.86[ASN][1000 genomes]
rs1673607	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673624	0.80[ASN][1000 genomes]
rs1679167	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1679175	0.90[ASN][1000 genomes]
rs1720836	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs2347469	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2881793	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3813264	0.87[TSI][hapmap]
rs4432674	0.86[ASN][1000 genomes]
rs4678264	1.00[ASN][1000 genomes]
rs4678265	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678420	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523975	0.82[CEU][hapmap]
rs550507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs559313	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs586946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60513493	0.86[ASN][1000 genomes]
rs611134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs629884	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs643620	0.82[CEU][hapmap]
rs6798058	0.80[ASN][1000 genomes]
rs680070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7625326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7634745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7643973	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7653815	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs773444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs773445	0.86[ASN][1000 genomes]
rs774003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs774004	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774006	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774007	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs774008	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774012	0.84[CEU][hapmap];0.89[TSI][hapmap]
rs808925	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811792	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811793	1.00[ASN][1000 genomes]
rs9811052	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9817419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9827256	0.93[ASN][1000 genomes]
rs9848718	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9848938	0.89[CEU][hapmap]
rs9853998	1.00[ASN][1000 genomes]
rs9855306	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs9878436	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9879213	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1679168	CEP70	cis	Muscle Skeletal	GTEx
rs1679168	CEP70	cis	Liver	GTEx
rs1679168	CEP70	cis	multi-tissue	Pritchard
rs1679168	CEP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
4	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
9	chr3:138179800-138199400	Weak transcription	Thymus	Thymus
10	chr3:138181200-138192400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:138184400-138198400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:138185000-138195200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:138187600-138197000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:138188000-138210800	Weak transcription	Lung	lung
15	chr3:138188000-138211600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:138188200-138196200	Strong transcription	Fetal Muscle Leg	muscle
17	chr3:138188200-138197400	Weak transcription	HSMM	muscle
18	chr3:138188200-138197600	Weak transcription	HSMMtube	muscle
19	chr3:138188400-138196400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:138189000-138195200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:138189000-138195400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:138189600-138198400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:138189800-138197800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:138190000-138194400	Weak transcription	Right Ventricle	heart
25	chr3:138190000-138210800	Weak transcription	Psoas Muscle	Psoas
26	chr3:138190200-138193400	Weak transcription	Fetal Heart	heart
27	chr3:138190800-138196200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:138191000-138193800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:138191200-138195800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:138191600-138195600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:138191800-138198600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:138191800-138203800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:138192000-138198400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links