Variant report

Variant	rs9288019
Chromosome Location	chr2:179276894-179276895
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr2:179276770-179277107	U2OS	brain:	n/a	n/a
2	POLR2A	chr2:179276854-179276942	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
2	chr2:179276440..179278357-chr2:179314496..179316084,2	MCF-7	breast:
3	chr2:179274878..179278568-chr2:179284211..179288261,3	K562	blood:
4	chr2:179269516..179271949-chr2:179276135..179277848,2	K562	blood:
5	chr2:179258451..179260379-chr2:179275317..179277044,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223960	TF binding region
ENSG00000155636	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10173183	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10179153	0.98[ASN][1000 genomes]
rs10201175	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10207436	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10930831	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11688081	0.88[EUR][1000 genomes]
rs12052983	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs13411588	0.84[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1559908	1.00[JPT][hapmap]
rs1560870	0.91[TSI][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	1.00[JPT][hapmap]
rs1978580	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2042996	0.84[JPT][hapmap]
rs2059691	0.85[JPT][hapmap]
rs2114581	0.91[TSI][hapmap]
rs2114582	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2249737	0.85[JPT][hapmap]
rs2276617	0.85[EUR][1000 genomes]
rs2288320	0.81[GIH][hapmap]
rs2288322	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2303536	1.00[JPT][hapmap]
rs2303537	1.00[JPT][hapmap]
rs2366601	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2366603	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2366604	0.93[ASN][1000 genomes]
rs2886712	0.84[ASN][1000 genomes]
rs3731750	0.84[JPT][hapmap]
rs3731754	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3752689	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769866	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4019558	0.91[TSI][hapmap]
rs4894017	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894018	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4894019	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4894020	0.84[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6704545	0.81[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6720559	0.83[YRI][hapmap]
rs6739142	0.84[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6753709	0.84[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs6757186	0.88[EUR][1000 genomes]
rs723841	0.85[EUR][1000 genomes]
rs728005	0.88[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7575643	1.00[JPT][hapmap]
rs7577862	1.00[JPT][hapmap]
rs7589565	0.95[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7589679	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598228	1.00[JPT][hapmap]
rs7600176	0.84[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs8179648	0.95[JPT][hapmap]
rs890579	0.94[ASW][hapmap];0.92[CEU][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs919177	0.88[EUR][1000 genomes]
rs957875	0.84[JPT][hapmap]
rs967507	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9967820	1.00[JPT][hapmap]
rs9973732	0.88[EUR][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	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9288019	FKBP7	cis	parietal	SCAN
rs9288019	PRKRA	cis	cerebellum	SCAN
rs9288019	FKBP7	cis	lymphoblastoid	seeQTL
rs9288019	CIR1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179269400-179277600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:179270000-179277800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:179270000-179277800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:179270600-179277800	Weak transcription	HSMM	muscle
5	chr2:179271000-179277000	Weak transcription	K562	blood
6	chr2:179271000-179277600	Weak transcription	GM12878-XiMat	blood
7	chr2:179271000-179277800	Weak transcription	HSMMtube	muscle
8	chr2:179272200-179277600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:179272200-179278000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:179276800-179277000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:179276800-179277200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:179276800-179277200	Enhancers	Fetal Intestine Small	intestine

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