Variant report

Variant	rs624486
Chromosome Location	chr15:40766879-40766880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10444792	0.86[EUR][1000 genomes]
rs10518696	0.86[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs11070276	0.87[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs11070278	0.86[EUR][1000 genomes]
rs11632319	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12442697	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12916218	0.87[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs1530942	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1530943	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs16970734	0.86[EUR][1000 genomes];0.93[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];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2014367	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2034653	0.81[EUR][1000 genomes]
rs2084941	0.84[EUR][1000 genomes]
rs2278887	0.94[GIH][hapmap]
rs2278889	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2290379	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2412528	0.86[EUR][1000 genomes]
rs2412530	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2924389	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2959535	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2959547	0.88[EUR][1000 genomes]
rs3803354	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4467046	0.81[EUR][1000 genomes]
rs4561439	0.81[EUR][1000 genomes]
rs4923873	0.86[EUR][1000 genomes]
rs4923877	0.87[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4923878	0.87[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4923879	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924473	0.88[EUR][1000 genomes]
rs4924474	0.88[EUR][1000 genomes]
rs4924476	0.88[EUR][1000 genomes]
rs4924482	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs4924483	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs582736	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs589650	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs607118	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611933	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]
rs617031	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs623187	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs639123	0.87[ASN][1000 genomes]
rs640919	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6492955	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs651131	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs667623	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]
rs7163648	0.81[EUR][1000 genomes]
rs7163889	0.81[EUR][1000 genomes]
rs7164056	0.81[EUR][1000 genomes]
rs7164166	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7164405	0.81[EUR][1000 genomes]
rs7167922	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7168913	0.81[EUR][1000 genomes]
rs7168927	0.88[EUR][1000 genomes]
rs7170073	0.81[EUR][1000 genomes]
rs7170327	0.81[EUR][1000 genomes]
rs7170946	0.81[EUR][1000 genomes]
rs8024579	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs8024802	0.87[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs8029208	0.86[EUR][1000 genomes]
rs8032453	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs8033739	0.88[EUR][1000 genomes]
rs8034726	0.87[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs8038350	0.82[EUR][1000 genomes]
rs8040187	0.87[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs8041816	0.87[CEU][hapmap]
rs8041991	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs8043197	0.88[EUR][1000 genomes]
rs896797	0.87[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs921624	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs9284288	0.88[EUR][1000 genomes]
rs976402	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs9783737	0.88[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs624486	CHP	cis	parietal	SCAN
rs624486	RPUSD2	cis	parietal	SCAN
rs624486	C15orf56	cis	parietal	SCAN
rs624486	NA	cis	multi-tissue	Pritchard
rs624486	C15orf57	cis	parietal	SCAN
rs624486	C15orf57	cis	cerebellum	SCAN

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

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