Variant report

Variant	rs7523787
Chromosome Location	chr1:94330615-94330616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94329412..94331639-chr1:94331729..94334290,2	K562	blood:
2	chr1:94326500..94334861-chr1:94334949..94340833,11	K562	blood:
3	chr1:94329330..94332326-chr1:94336085..94338247,2	MCF-7	breast:
4	chr1:94330084..94332502-chr1:94374420..94376591,2	K562	blood:
5	chr1:94310322..94313245-chr1:94329238..94330853,2	MCF-7	breast:
6	chr1:94330084..94333189-chr1:94373240..94377284,3	K562	blood:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10874797	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164970	0.82[EUR][1000 genomes]
rs11164973	0.87[EUR][1000 genomes]
rs11164974	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11165021	0.80[EUR][1000 genomes]
rs11165022	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11165023	0.80[EUR][1000 genomes]
rs11165026	0.82[CEU][hapmap]
rs11582870	0.90[EUR][1000 genomes]
rs12029548	0.80[EUR][1000 genomes]
rs12758972	0.80[EUR][1000 genomes]
rs1884019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092698	0.80[EUR][1000 genomes]
rs2092699	0.80[EUR][1000 genomes]
rs2092700	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2103784	0.80[EUR][1000 genomes]
rs2143991	0.94[ASN][1000 genomes]
rs2143992	0.82[CEU][hapmap]
rs2235970	0.84[JPT][hapmap]
rs2301022	0.94[JPT][hapmap]
rs2391315	0.82[CEU][hapmap]
rs2391321	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2747036	0.90[EUR][1000 genomes]
rs2747037	0.90[EUR][1000 genomes]
rs2747038	0.89[EUR][1000 genomes]
rs2747040	0.89[EUR][1000 genomes]
rs2747042	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2747044	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2747047	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2747049	0.90[EUR][1000 genomes]
rs2818161	0.83[EUR][1000 genomes]
rs2818165	0.90[EUR][1000 genomes]
rs2818166	0.89[EUR][1000 genomes]
rs2818167	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789453	0.94[JPT][hapmap]
rs3789457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4520428	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4847184	0.89[EUR][1000 genomes]
rs4847191	0.80[EUR][1000 genomes]
rs4847192	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847254	0.89[EUR][1000 genomes]
rs4847257	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4847263	0.80[EUR][1000 genomes]
rs4847264	0.82[CEU][hapmap]
rs6541399	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6660210	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666633	0.80[EUR][1000 genomes]
rs6667986	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6681169	0.80[EUR][1000 genomes]
rs6681265	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs6684054	0.80[EUR][1000 genomes]
rs6703684	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs743110	0.81[GIH][hapmap];0.94[JPT][hapmap]
rs7517632	0.80[EUR][1000 genomes]
rs7518940	0.80[EUR][1000 genomes]
rs7526082	0.99[ASN][1000 genomes]
rs7552293	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555136	0.80[EUR][1000 genomes]
rs947343	0.89[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	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7523787	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7523787	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs7523787	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs7523787	RP11-488P3.1	cis	Artery Tibial	GTEx
rs7523787	RP11-488P3.1	cis	lung	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94314200-94332800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:94314200-94334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:94314200-94334400	Weak transcription	Brain Substantia Nigra	brain
4	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:94322600-94334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:94328800-94334800	Weak transcription	Hela-S3	cervix
7	chr1:94329400-94334600	Weak transcription	A549	lung
8	chr1:94329600-94334000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:94329800-94333200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:94329800-94335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:94330000-94332800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:94330000-94333600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:94330000-94334200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:94330000-94334200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:94330000-94334600	Weak transcription	K562	blood
17	chr1:94330000-94337000	Weak transcription	Psoas Muscle	Psoas
18	chr1:94330000-94338800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:94330200-94334200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:94330200-94334600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:94330400-94332800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:94330400-94334600	Weak transcription	HUVEC	blood vessel
23	chr1:94330600-94332400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:94330600-94334200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:94330600-94334600	Weak transcription	HSMM	muscle
26	chr1:94330600-94335200	Weak transcription	NHLF	lung
27	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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