Variant report

Variant	rs7546890
Chromosome Location	chr1:160995392-160995393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160963251..160966052-chr1:160993360..160995980,2	K562	blood:
2	chr1:160989659..160993154-chr1:160993491..160996992,5	K562	blood:
3	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158769	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000215845	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1023115	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs12030262	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12723902	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12743772	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243479	0.82[ASN][1000 genomes]
rs2246139	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2250288	0.87[ASN][1000 genomes]
rs2256633	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2481072	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483143	0.85[ASN][1000 genomes]
rs2483144	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483148	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28365978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2988723	0.87[ASN][1000 genomes]
rs2990700	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2990701	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990704	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990705	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007156	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007157	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656975	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530765	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9427367	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7546890	ASH1L	cis	cerebellum	SCAN
rs7546890	CD1A	cis	parietal	SCAN
rs7546890	F11R	cis	parietal	SCAN
rs7546890	F11R	cis	cerebellum	SCAN
rs7546890	F11R	cis	Thyroid	GTEx
rs7546890	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs7546890	APOA2	cis	cerebellum	SCAN
rs7546890	ARHGEF11	cis	cerebellum	SCAN
rs7546890	HDGF	cis	cerebellum	SCAN
rs7546890	USF1	cis	multi-tissue	Pritchard
rs7546890	MNDA	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160991200-161007800	Weak transcription	HSMMtube	muscle
2	chr1:160991600-161002400	Weak transcription	Ovary	ovary
3	chr1:160991600-161007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:160991800-160997000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:160991800-161004600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:160991800-161005200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:160991800-161007600	Weak transcription	Thymus	Thymus
8	chr1:160991800-161007800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:160992000-161001600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:160992000-161002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:160992000-161002200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:160992000-161004600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:160992000-161007000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:160992200-161008000	Weak transcription	HUVEC	blood vessel
15	chr1:160992400-161002400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:160992800-160996600	Weak transcription	A549	lung
17	chr1:160992800-161002200	Weak transcription	NHEK	skin
18	chr1:160995000-160995600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:160995200-160995400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:160995200-160995600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:160995200-160995600	Enhancers	HSMM	muscle
22	chr1:160995200-160995600	Enhancers	K562	blood
23	chr1:160995200-160995800	Enhancers	Primary neutrophils fromperipheralblood	blood

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