Variant report

Variant	rs35684277
Chromosome Location	chr15:40955069-40955070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40938971..40941359-chr15:40954270..40956007,2	MCF-7	breast:
2	chr15:40954350..40957294-chr15:40985826..40987543,2	K562	blood:

Variant related genes	Relation type
ENSG00000245849	Chromatin interaction
ENSG00000137812	Chromatin interaction
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10152546	0.84[EUR][1000 genomes]
rs1044474	0.81[EUR][1000 genomes]
rs10518697	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1058734	0.85[EUR][1000 genomes]
rs11070283	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11630273	0.89[EUR][1000 genomes]
rs11633184	0.87[EUR][1000 genomes]
rs11637245	0.83[EUR][1000 genomes]
rs11637422	0.86[EUR][1000 genomes]
rs12148915	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12324748	0.87[EUR][1000 genomes]
rs12385982	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441754	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12442560	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12591044	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12592524	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12903817	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907442	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908316	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913296	0.84[EUR][1000 genomes]
rs12913739	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915171	0.84[EUR][1000 genomes]
rs12915636	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17673703	0.84[EUR][1000 genomes]
rs17674454	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17747423	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17747633	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1801321	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1814541	0.89[EUR][1000 genomes]
rs2412525	0.86[EUR][1000 genomes]
rs2619682	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28529389	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28634695	0.84[EUR][1000 genomes]
rs28669075	0.84[EUR][1000 genomes]
rs28866515	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28891195	0.90[AMR][1000 genomes]
rs34305357	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34739056	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824658	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127391	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35842610	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4923880	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924486	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924492	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924496	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4924502	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5030789	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59244061	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62019876	0.87[EUR][1000 genomes]
rs62019879	0.89[EUR][1000 genomes]
rs71471880	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165509	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170288	0.86[EUR][1000 genomes]
rs7175747	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176245	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7176590	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7177265	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7180135	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7182499	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8029530	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036891	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037180	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038122	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042386	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957603	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9920642	0.86[EUR][1000 genomes]
rs9920676	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs35684277	C15orf57	cis	lung	GTEx
rs35684277	C15orf57	cis	Stomach	GTEx
rs35684277	C15orf57	cis	Adipose Subcutaneous	GTEx
rs35684277	C15orf57	cis	Heart Left Ventricle	GTEx
rs35684277	RP11-111A22.1	cis	lung	GTEx
rs35684277	C15orf57	cis	Esophagus Muscularis	GTEx
rs35684277	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs35684277	C15orf57	cis	Nerve Tibial	GTEx
rs35684277	RP11-111A22.1	cis	Artery Tibial	GTEx
rs35684277	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs35684277	C15orf57	cis	Esophagus Mucosa	GTEx
rs35684277	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs35684277	RAD51	cis	multi-tissue	Pritchard
rs35684277	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs35684277	CCDC32	cis	multi-tissue	Pritchard
rs35684277	RP11-111A22.1	cis	Artery Aorta	GTEx
rs35684277	C15orf57	cis	Muscle Skeletal	GTEx
rs35684277	C15orf57	cis	Artery Tibial	GTEx
rs35684277	C15orf57	cis	Artery Aorta	GTEx
rs35684277	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
5	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
8	chr15:40913800-40986000	Weak transcription	A549	lung
9	chr15:40914400-40960000	Weak transcription	NHLF	lung
10	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
12	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
14	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
16	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:40939800-40956800	Strong transcription	Dnd41	blood
19	chr15:40939800-40956800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:40941400-40957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:40942000-40959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:40942200-40955800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:40942600-40955800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:40943000-40956000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:40943000-40956000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
27	chr15:40944600-40955200	Strong transcription	Thymus	Thymus
28	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:40945200-40961400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:40946600-40957600	Weak transcription	HSMM	muscle
31	chr15:40946600-40957600	Weak transcription	NH-A	brain
32	chr15:40946600-40959800	Weak transcription	Gastric	stomach
33	chr15:40947600-40956400	Weak transcription	HMEC	breast
34	chr15:40949200-40957400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:40949400-40955200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:40949600-40955200	Strong transcription	Fetal Stomach	stomach
37	chr15:40949800-40956400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:40949800-40956600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:40950000-40958600	Weak transcription	HUVEC	blood vessel
40	chr15:40950000-40958800	Weak transcription	HepG2	liver
41	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:40950200-40964200	Weak transcription	Osteobl	bone
43	chr15:40951000-40955200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:40951400-40955200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:40951400-40955400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:40951600-40955200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:40951600-40955200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:40951800-40957800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:40952200-40955600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:40953000-40955200	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links