Variant report

Variant	rs17660531
Chromosome Location	chr1:76547750-76547751
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	chr1:76538798..76540470-chr1:76545089..76547752,3	K562	blood:
2	chr1:76540930..76543846-chr1:76546687..76549468,2	K562	blood:

Variant related genes	Relation type
ENSG00000184005	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1146660	0.89[CEU][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1146664	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1146665	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11585383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251464	0.94[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs1251465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1251569	1.00[YRI][hapmap]
rs1251577	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1251578	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1335740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17660501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55811448	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56320696	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61771321	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692547	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535776	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7545733	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17660531	FAM73A	cis	parietal	SCAN
rs17660531	PIGK	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76541200-76551200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:76541600-76548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:76541600-76550000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:76542200-76553200	Weak transcription	Fetal Intestine Large	intestine
5	chr1:76542400-76550000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
7	chr1:76545200-76548600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:76545200-76548800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:76545400-76551400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:76545600-76548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:76545600-76548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:76545600-76548600	Enhancers	Brain Substantia Nigra	brain
13	chr1:76545600-76549000	Weak transcription	Lung	lung
14	chr1:76545600-76552200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:76545600-76558200	Weak transcription	Left Ventricle	heart
16	chr1:76545800-76548000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:76545800-76550600	Enhancers	Fetal Lung	lung
18	chr1:76546000-76548000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:76546200-76547800	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:76546200-76550600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:76546400-76548800	Enhancers	Brain Cingulate Gyrus	brain
22	chr1:76546400-76549000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:76546600-76548400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:76546600-76549200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:76546800-76547800	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:76546800-76548000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:76546800-76548800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:76547000-76549000	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:76547200-76548000	Enhancers	Fetal Brain Female	brain
30	chr1:76547400-76548800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:76547400-76548800	Enhancers	Brain Anterior Caudate	brain
32	chr1:76547400-76549200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:76547400-76549200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:76547400-76549200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:76547400-76552200	Weak transcription	Fetal Kidney	kidney
36	chr1:76547600-76547800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:76547600-76548200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr1:76547600-76548200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:76547600-76548400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:76547600-76549000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:76547600-76549200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr1:76547600-76549200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:76547600-76550000	Weak transcription	Fetal Stomach	stomach

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