Variant report

Variant	rs655003
Chromosome Location	chr15:42411242-42411243
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42398541..42400541-chr15:42411116..42413868,2	K562	blood:
2	chr15:42359873..42362452-chr15:42410836..42413040,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10518751	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852412	1.00[ASN][1000 genomes]
rs1712439	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591581	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601823	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs613426	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667758	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687352	0.87[ASN][1000 genomes]
rs694980	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776707	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776710	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776713	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776715	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776717	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv457121	chr15:42396282-42418085	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv569236	chr15:42396282-42418085	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs655003	EHD4	cis	cerebellum	SCAN
rs655003	RTF1	cis	cerebellum	SCAN
rs655003	PLA2G4D	cis	Esophagus Mucosa	GTEx
rs655003	LRRC57	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42405000-42411400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:42410600-42411800	Enhancers	H9 Cell Line	embryonic stem cell
3	chr15:42410600-42411800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr15:42410800-42411400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:42410800-42411600	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr15:42410800-42412000	Enhancers	Stomach Mucosa	stomach
7	chr15:42410800-42412000	Bivalent Enhancer	HepG2	liver
8	chr15:42410800-42416000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:42411000-42411400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:42411000-42411400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr15:42411000-42411400	Enhancers	NHEK	skin
12	chr15:42411000-42411600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:42411000-42411600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr15:42411000-42411600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:42411000-42411600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:42411000-42411600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr15:42411000-42411600	Enhancers	Right Atrium	heart
18	chr15:42411000-42411600	Enhancers	Thymus	Thymus
19	chr15:42411000-42411800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr15:42411000-42412000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr15:42411000-42412000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:42411000-42412000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:42411000-42412000	Enhancers	Fetal Muscle Leg	muscle
24	chr15:42411000-42412000	Enhancers	Fetal Stomach	stomach
25	chr15:42411000-42412000	Enhancers	Lung	lung
26	chr15:42411000-42412000	Enhancers	Pancreas	Pancrea
27	chr15:42411000-42412000	Flanking Active TSS	Dnd41	blood
28	chr15:42411000-42414000	Enhancers	Fetal Intestine Small	intestine
29	chr15:42411200-42411400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr15:42411200-42411400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:42411200-42411400	Active TSS	Duodenum Mucosa	Duodenum
32	chr15:42411200-42411400	Active TSS	Esophagus	oesophagus
33	chr15:42411200-42411400	Enhancers	Fetal Intestine Large	intestine
34	chr15:42411200-42411400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr15:42411200-42411400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr15:42411200-42411600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:42411200-42411600	Weak transcription	Fetal Heart	heart
38	chr15:42411200-42411600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr15:42411200-42411600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr15:42411200-42411800	Flanking Active TSS	Fetal Thymus	thymus
41	chr15:42411200-42412000	Enhancers	Adipose Nuclei	Adipose
42	chr15:42411200-42412000	Active TSS	Rectal Smooth Muscle	rectum
43	chr15:42411200-42415800	Enhancers	Primary neutrophils fromperipheralblood	blood

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