Variant report

Variant	rs7548665
Chromosome Location	chr1:220468502-220468503
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220466641..220469132-chr1:220471949..220474218,2	K562	blood:
2	chr1:220462922..220464808-chr1:220468310..220469858,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10495146	0.93[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11118520	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11799636	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803993	0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11810365	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11812073	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12561809	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12568605	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13373856	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13373866	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13374049	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13374288	0.88[AMR][1000 genomes]
rs13375365	0.88[AMR][1000 genomes]
rs1397959	0.93[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1397960	0.93[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17007380	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17007446	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17007454	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17007467	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17007481	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17007483	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2048478	0.93[JPT][hapmap]
rs2048479	0.81[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2048480	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2102571	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2137114	0.81[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes]
rs2667965	0.80[ASN][1000 genomes]
rs2814497	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34368227	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34567692	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34622636	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34870946	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4460644	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4846310	0.88[CHD][hapmap]
rs4846312	0.94[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4846313	0.80[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4846315	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4846624	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4846625	0.88[AMR][1000 genomes]
rs5015199	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5015200	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5015201	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5015202	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5015203	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5015204	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55917547	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59417140	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60882165	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60892757	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6541129	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6541131	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6541132	0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6541133	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6541134	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6541135	0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6541136	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6541137	0.80[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6656323	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6657742	0.81[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6660564	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662971	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663091	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663291	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664646	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6671030	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6673482	0.81[CEU][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6681814	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682177	0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6682555	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6683491	0.93[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6689931	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690030	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6694670	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695480	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696262	0.89[ASN][1000 genomes]
rs6701905	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6702336	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73092104	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73102580	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74139021	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74142205	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7514723	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7522167	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7532956	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7540014	0.82[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540608	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545196	0.81[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7553951	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907416	0.81[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7548665	SPECC1	trans	lymphoblastoid	seeQTL
rs7548665	COL4A1	trans	lymphoblastoid	seeQTL
rs7548665	HECW2	trans	lymphoblastoid	seeQTL
rs7548665	CYP1B1	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220464200-220470400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:220464200-220473600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:220464600-220471600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:220464600-220471600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:220464600-220473800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:220465200-220472600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:220466600-220468600	Enhancers	Fetal Stomach	stomach
8	chr1:220466800-220468600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:220467200-220469200	Enhancers	NHDF-Ad	bronchial
10	chr1:220467400-220468600	Enhancers	Osteobl	bone
11	chr1:220467400-220471200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:220467400-220472200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:220467800-220468600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:220467800-220468600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:220468000-220468600	Enhancers	NH-A	brain
16	chr1:220468200-220468600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:220468400-220468600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:220468400-220471200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:220468400-220471400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:220468400-220473600	Weak transcription	Rectal Smooth Muscle	rectum

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