Variant report

Variant	rs28634695
Chromosome Location	chr15:40856113-40856114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40854296..40857804-chr15:40884735..40887632,3	K562	blood:
2	chr15:40855952..40857673-chr15:41046204..41048687,2	K562	blood:
3	chr15:40855657..40859262-chr15:40860971..40863634,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166133	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152546	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1044474	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518697	0.90[EUR][1000 genomes]
rs1058734	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070283	0.89[EUR][1000 genomes]
rs11630273	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11633184	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637245	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637422	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324748	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12385982	0.89[EUR][1000 genomes]
rs12441754	0.81[EUR][1000 genomes]
rs12903817	0.85[EUR][1000 genomes]
rs12908316	0.87[EUR][1000 genomes]
rs12913296	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913739	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12915171	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915636	0.90[EUR][1000 genomes]
rs13329076	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673703	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17674454	0.89[EUR][1000 genomes]
rs17747423	0.90[EUR][1000 genomes]
rs17747633	0.90[EUR][1000 genomes]
rs1814541	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2412525	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28647196	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669075	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34739056	0.80[EUR][1000 genomes]
rs34824658	0.86[EUR][1000 genomes]
rs35127391	0.92[EUR][1000 genomes]
rs35684277	0.84[EUR][1000 genomes]
rs35842610	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4923880	0.88[EUR][1000 genomes]
rs4924486	0.88[EUR][1000 genomes]
rs62019876	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62019879	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71471880	0.84[EUR][1000 genomes]
rs7165509	0.84[EUR][1000 genomes]
rs7170288	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175747	0.83[EUR][1000 genomes]
rs8029530	0.80[EUR][1000 genomes]
rs8036891	0.80[EUR][1000 genomes]
rs8037180	0.82[EUR][1000 genomes]
rs8038122	0.84[EUR][1000 genomes]
rs8042386	0.82[EUR][1000 genomes]
rs9920642	0.84[EUR][1000 genomes]
rs9920676	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs28634695	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs28634695	C15orf57	cis	lung	GTEx
rs28634695	C15orf57	cis	Muscle Skeletal	GTEx
rs28634695	RP11-111A22.1	cis	Artery Tibial	GTEx
rs28634695	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs28634695	C15orf57	cis	Stomach	GTEx
rs28634695	RP11-111A22.1	cis	Artery Aorta	GTEx
rs28634695	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs28634695	C15orf57	cis	Adipose Subcutaneous	GTEx
rs28634695	C15orf57	cis	Esophagus Mucosa	GTEx
rs28634695	C15orf57	cis	Artery Aorta	GTEx
rs28634695	C15orf57	cis	Artery Tibial	GTEx
rs28634695	RP11-111A22.1	cis	lung	GTEx
rs28634695	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs28634695	C15orf57	cis	Heart Left Ventricle	GTEx
rs28634695	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs28634695	C15orf57	cis	Esophagus Muscularis	GTEx
rs28634695	C15orf57	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
3	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40838000-40856400	Weak transcription	A549	lung
6	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
7	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
9	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
10	chr15:40843800-40856400	Weak transcription	HSMMtube	muscle
11	chr15:40846200-40856200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:40846600-40856400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:40846600-40856400	Weak transcription	Right Atrium	heart
14	chr15:40846600-40856600	Weak transcription	Aorta	Aorta
15	chr15:40846600-40856600	Weak transcription	Gastric	stomach
16	chr15:40847200-40856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:40847400-40856200	Weak transcription	Brain Germinal Matrix	brain
18	chr15:40847400-40856400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:40847400-40856600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:40848000-40856400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:40848000-40856400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:40848000-40856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:40848000-40856400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:40848400-40856400	Weak transcription	NHDF-Ad	bronchial
25	chr15:40848600-40856200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:40848600-40856200	Weak transcription	HSMM	muscle
27	chr15:40848600-40856200	Weak transcription	HUVEC	blood vessel
28	chr15:40848600-40856200	Weak transcription	NHLF	lung
29	chr15:40848600-40856400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:40848600-40856400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:40848600-40856400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:40848600-40856400	Weak transcription	Brain Substantia Nigra	brain
33	chr15:40848600-40856400	Weak transcription	NH-A	brain
34	chr15:40848800-40856200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:40848800-40856400	Weak transcription	Brain Angular Gyrus	brain
36	chr15:40848800-40856600	Weak transcription	Lung	lung
37	chr15:40849000-40856400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:40849000-40856600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:40849400-40856400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:40849600-40856200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:40849600-40856200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:40849600-40856400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:40850000-40856200	Weak transcription	Placenta	Placenta
44	chr15:40850000-40856400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:40850000-40856400	Weak transcription	Fetal Kidney	kidney
46	chr15:40850200-40856400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:40851000-40856400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:40851400-40856200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:40851800-40856600	Weak transcription	Esophagus	oesophagus
50	chr15:40854200-40856200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links