Variant report

Variant	rs6754662
Chromosome Location	chr2:9890152-9890153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9843332..9845543-chr2:9887968..9890552,2	K562	blood:
2	chr2:9887703..9890322-chr2:9895249..9898241,2	MCF-7	breast:
3	chr2:9888046..9890254-chr2:9893584..9895138,2	K562	blood:
4	chr2:9877856..9880099-chr2:9889992..9892399,2	K562	blood:
5	chr2:9881091..9883145-chr2:9887782..9890192,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10171491	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10173057	0.89[ASN][1000 genomes]
rs10176382	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10178017	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180724	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200779	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10200869	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10202283	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929607	0.83[ASN][1000 genomes]
rs10929608	0.83[ASN][1000 genomes]
rs10929609	0.83[ASN][1000 genomes]
rs1110317	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1123269	0.80[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11674024	0.90[ASN][1000 genomes]
rs11674642	0.95[JPT][hapmap]
rs11676286	0.90[ASN][1000 genomes]
rs11678697	0.89[ASN][1000 genomes]
rs11680429	0.95[JPT][hapmap]
rs12470409	0.90[ASN][1000 genomes]
rs12475853	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12476199	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12476232	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12692393	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692394	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12996417	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13018695	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13028425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13395171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554107	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1554108	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357263	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs34491197	0.84[ASN][1000 genomes]
rs4668636	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4668637	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4668644	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669427	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4669428	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4669429	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4669445	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4669447	0.83[ASN][1000 genomes]
rs4669448	0.90[ASN][1000 genomes]
rs4669451	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6432033	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6708081	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6713497	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735280	0.95[JPT][hapmap]
rs6740013	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6742929	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743152	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6756567	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6761286	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761920	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7423455	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7423458	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602784	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs7605675	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs868442	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6754662	PDIA6	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9880200-9892800	Weak transcription	Thymus	Thymus
2	chr2:9880200-9893200	Weak transcription	Right Atrium	heart
3	chr2:9884800-9892600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:9885200-9891200	Weak transcription	Right Ventricle	heart
5	chr2:9885200-9891400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:9885200-9893000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:9885400-9891000	Weak transcription	Psoas Muscle	Psoas
8	chr2:9885400-9893000	Weak transcription	Left Ventricle	heart
9	chr2:9885600-9892600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:9885800-9891000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:9885800-9891600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:9886000-9891600	Weak transcription	NHDF-Ad	bronchial
13	chr2:9886200-9892800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:9888600-9892000	Enhancers	Fetal Muscle Leg	muscle
15	chr2:9888600-9893000	Enhancers	GM12878-XiMat	blood
16	chr2:9889000-9890400	Enhancers	HSMMtube	muscle
17	chr2:9889200-9891800	Weak transcription	Hela-S3	cervix
18	chr2:9889200-9891800	Weak transcription	NHEK	skin
19	chr2:9889200-9892400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:9889400-9890600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:9889400-9890800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:9889400-9892000	Weak transcription	HMEC	breast
23	chr2:9889400-9892600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:9889400-9893200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:9889600-9890800	Weak transcription	Fetal Heart	heart
26	chr2:9889600-9891000	Weak transcription	A549	lung
27	chr2:9889800-9896800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:9890000-9890200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:9890000-9892600	Weak transcription	Fetal Intestine Large	intestine
30	chr2:9890000-9892600	Weak transcription	HSMM	muscle

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