Variant report

Variant	rs667623
Chromosome Location	chr15:40765360-40765361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40731621..40739951-chr15:40753297..40765462,23	K562	blood:
2	chr15:40763768..40766540-chr15:40784281..40786409,2	K562	blood:
3	chr15:40764613..40768482-chr15:40771207..40776375,6	K562	blood:
4	chr15:40761789..40767637-chr15:40797359..40801640,7	K562	blood:
5	chr15:40721609..40724539-chr15:40764189..40766844,2	K562	blood:
6	chr15:40763301..40766173-chr15:40861522..40864181,2	K562	blood:
7	chr15:40731823..40734826-chr15:40760868..40766207,7	K562	blood:
8	chr15:40757699..40759637-chr15:40765203..40767297,2	MCF-7	breast:
9	chr15:40763466..40765784-chr15:40773295..40775990,2	MCF-7	breast:
10	chr15:40721609..40723938-chr15:40763922..40765689,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259536	Chromatin interaction
ENSG00000166133	Chromatin interaction
ENSG00000259211	Chromatin interaction
ENSG00000140320	Chromatin interaction
ENSG00000244251	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10444792	0.81[EUR][1000 genomes]
rs10518696	0.88[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs11070276	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11070278	0.81[EUR][1000 genomes]
rs11632319	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs12442697	0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs12916218	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1530942	0.82[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs1530943	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs16970734	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16970854	0.88[JPT][hapmap]
rs1869303	0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2014367	0.84[JPT][hapmap]
rs2034653	0.86[JPT][hapmap]
rs2084941	0.82[EUR][1000 genomes]
rs2278887	0.94[GIH][hapmap];0.88[JPT][hapmap]
rs2278889	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2290379	0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs2412528	0.82[EUR][1000 genomes]
rs2412530	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2924389	0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs2959535	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2959547	0.83[EUR][1000 genomes]
rs3803354	0.88[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs4467046	0.88[JPT][hapmap]
rs4923873	0.82[EUR][1000 genomes]
rs4923877	0.88[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs4923878	0.88[GIH][hapmap];0.86[TSI][hapmap]
rs4923879	0.88[JPT][hapmap]
rs4924473	0.83[EUR][1000 genomes]
rs4924474	0.83[EUR][1000 genomes]
rs4924476	0.83[EUR][1000 genomes]
rs4924482	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs4924483	0.88[JPT][hapmap]
rs582736	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs589650	0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs607118	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs611933	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617031	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs623187	0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs624486	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639123	0.85[ASN][1000 genomes]
rs640919	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492955	0.88[JPT][hapmap]
rs651131	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7164166	0.88[JPT][hapmap]
rs7168927	0.83[EUR][1000 genomes]
rs8024579	0.88[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs8024802	0.88[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs8029208	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs8033739	0.83[EUR][1000 genomes]
rs8034726	0.82[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs8040187	0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs8041816	0.82[JPT][hapmap]
rs8041991	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs8043197	0.83[EUR][1000 genomes]
rs896797	0.88[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs921624	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs9284288	0.83[EUR][1000 genomes]
rs976402	0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap]
rs9783737	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs667623	C15orf57	cis	cerebellum	SCAN
rs667623	CHP	cis	parietal	SCAN
rs667623	C15orf57	cis	parietal	SCAN
rs667623	RPUSD2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40763000-40770200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40764400-40765600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:40764600-40765400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:40764600-40765600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr15:40764600-40765600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr15:40764600-40765600	Enhancers	Dnd41	blood
7	chr15:40764600-40766400	Weak transcription	Fetal Brain Male	brain
8	chr15:40764600-40766800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:40764600-40766800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:40764600-40767000	Weak transcription	Fetal Intestine Small	intestine
11	chr15:40764600-40768200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:40764600-40769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:40764600-40770000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:40764600-40770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:40764600-40771400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:40764800-40765400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:40764800-40765400	Enhancers	Fetal Muscle Leg	muscle
18	chr15:40764800-40765600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:40764800-40766400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:40764800-40767000	Weak transcription	Fetal Intestine Large	intestine
21	chr15:40764800-40767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:40764800-40770000	Weak transcription	NHEK	skin
23	chr15:40765000-40765600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:40765000-40766200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:40765000-40766400	Weak transcription	Fetal Thymus	thymus
26	chr15:40765000-40766600	Weak transcription	K562	blood
27	chr15:40765000-40767000	Weak transcription	Brain Germinal Matrix	brain
28	chr15:40765000-40767200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:40765000-40767200	Strong transcription	Fetal Stomach	stomach
30	chr15:40765000-40767600	Weak transcription	Primary T cells from cord blood	blood
31	chr15:40765000-40769800	Weak transcription	Hela-S3	cervix
32	chr15:40765000-40772400	Weak transcription	Esophagus	oesophagus
33	chr15:40765000-40773400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:40765200-40765400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:40765200-40766000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:40765200-40766200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:40765200-40766600	Weak transcription	Thymus	Thymus
38	chr15:40765200-40767000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:40765200-40768400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:40765200-40770200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:40765200-40770800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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