Variant report

Variant	rs1998458
Chromosome Location	chr6:118260565-118260566
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	chr6:118253546..118255566-chr6:118258595..118261283,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10457323	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10457324	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10499084	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11153710	0.86[CHB][hapmap]
rs1160428	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11754631	0.93[CHB][hapmap]
rs12206792	0.88[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs12212649	0.82[EUR][1000 genomes]
rs1323100	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1323101	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1338968	0.84[JPT][hapmap]
rs1338974	1.00[CHB][hapmap]
rs1338975	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361288	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs1416416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1416417	0.86[CHB][hapmap]
rs1416418	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1416419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1416420	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1416421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1416422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1538455	0.84[CEU][hapmap]
rs1570447	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1980748	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2211098	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2355792	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2760240	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs2789010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2789013	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4946304	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6568991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6937496	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7738597	0.86[CHB][hapmap]
rs7775647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs912088	0.94[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9320623	0.85[GIH][hapmap]
rs9320624	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9372488	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9374691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9385027	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9387524	0.85[ASN][1000 genomes]
rs9387531	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9387535	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs9398468	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9401040	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs9401044	0.94[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs9401046	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9489295	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs982647	0.84[CEU][hapmap];0.83[TSI][hapmap]

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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1998458	LCK	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118259000-118260600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:118259000-118260600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr6:118259000-118260600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr6:118259000-118260600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:118259000-118261400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:118259200-118261200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:118259400-118260600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:118259400-118260800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:118259800-118266800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:118260000-118261000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:118260200-118266800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:118260200-118268200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:118260400-118265200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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