Variant report

Variant	rs611933
Chromosome Location	chr15:40766442-40766443
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40763768..40766540-chr15:40784281..40786409,2	K562	blood:
2	chr15:40764613..40768482-chr15:40771207..40776375,6	K562	blood:
3	chr15:40761789..40767637-chr15:40797359..40801640,7	K562	blood:
4	chr15:40743208..40745711-chr15:40766264..40768804,2	MCF-7	breast:
5	chr15:40721609..40724539-chr15:40764189..40766844,2	K562	blood:
6	chr15:40765795..40768318-chr15:40771145..40773484,3	MCF-7	breast:
7	chr15:40757699..40759637-chr15:40765203..40767297,2	MCF-7	breast:

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

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10444792	0.85[EUR][1000 genomes]
rs10518696	0.86[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap]
rs11070276	0.87[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs11070278	0.85[EUR][1000 genomes]
rs11632319	0.85[CEU][hapmap]
rs12442697	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs12916218	0.86[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1530942	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1530943	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs16970734	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16970854	0.87[CEU][hapmap]
rs1869303	0.87[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2014367	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2084941	0.85[EUR][1000 genomes]
rs2278887	0.94[GIH][hapmap]
rs2278889	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2290379	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap]
rs2412528	0.85[EUR][1000 genomes]
rs2412530	0.87[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2924389	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs2959535	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2959547	0.86[EUR][1000 genomes]
rs3803354	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4923873	0.85[EUR][1000 genomes]
rs4923877	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs4923878	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs4923879	0.86[CEU][hapmap]
rs4924473	0.86[EUR][1000 genomes]
rs4924474	0.86[EUR][1000 genomes]
rs4924476	0.86[EUR][1000 genomes]
rs4924482	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs4924483	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs582736	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs589650	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs607118	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs617031	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs623187	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs624486	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639123	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs640919	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492955	0.87[CEU][hapmap]
rs651131	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs667623	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]
rs7164166	0.87[CEU][hapmap]
rs7167922	0.87[CEU][hapmap]
rs7168927	0.86[EUR][1000 genomes]
rs8024579	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs8024802	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs8029208	0.85[EUR][1000 genomes]
rs8032453	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs8033739	0.86[EUR][1000 genomes]
rs8034726	0.87[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap]
rs8038350	0.80[EUR][1000 genomes]
rs8040187	0.86[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs8041816	0.86[CEU][hapmap]
rs8041991	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs8043197	0.86[EUR][1000 genomes]
rs896797	0.87[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs921624	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9284288	0.86[EUR][1000 genomes]
rs976402	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs9783737	0.86[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs611933	CHP	cis	parietal	SCAN
rs611933	C15orf56	cis	parietal	SCAN
rs611933	C15orf57	cis	cerebellum	SCAN
rs611933	RPUSD2	cis	parietal	SCAN
rs611933	C15orf57	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr15:40764600-40766800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:40764600-40766800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:40764600-40767000	Weak transcription	Fetal Intestine Small	intestine
5	chr15:40764600-40768200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:40764600-40769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:40764600-40770000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:40764600-40770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:40764600-40771400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:40764800-40767000	Weak transcription	Fetal Intestine Large	intestine
11	chr15:40764800-40767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:40764800-40770000	Weak transcription	NHEK	skin
13	chr15:40765000-40766600	Weak transcription	K562	blood
14	chr15:40765000-40767000	Weak transcription	Brain Germinal Matrix	brain
15	chr15:40765000-40767200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:40765000-40767200	Strong transcription	Fetal Stomach	stomach
17	chr15:40765000-40767600	Weak transcription	Primary T cells from cord blood	blood
18	chr15:40765000-40769800	Weak transcription	Hela-S3	cervix
19	chr15:40765000-40772400	Weak transcription	Esophagus	oesophagus
20	chr15:40765000-40773400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:40765200-40766600	Weak transcription	Thymus	Thymus
22	chr15:40765200-40767000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:40765200-40768400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:40765200-40770200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:40765200-40770800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:40765600-40768400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:40766400-40766600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:40766400-40766600	Enhancers	Fetal Thymus	thymus
29	chr15:40766400-40766600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr15:40766400-40767200	Enhancers	Fetal Muscle Leg	muscle

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