Variant report

Variant	rs10924866
Chromosome Location	chr1:247084871-247084872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247074467..247081092-chr1:247083777..247087568,7	K562	blood:
2	chr1:247082517..247086516-chr1:247093624..247096461,4	MCF-7	breast:
3	chr1:247083293..247084888-chr1:247092753..247095092,2	MCF-7	breast:
4	chr1:247025253..247030388-chr1:247080554..247085135,5	K562	blood:

Variant related genes	Relation type
ENSG00000153207	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10436931	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10924862	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10924863	0.81[EUR][1000 genomes]
rs10924867	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10924869	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11585265	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023594	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033144	0.91[AFR][1000 genomes]
rs12033829	0.82[AFR][1000 genomes]
rs12691532	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12728361	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12739487	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12739603	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12748665	0.84[AFR][1000 genomes]
rs12752855	0.81[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs1892116	1.00[ASW][hapmap];0.81[CEU][hapmap];0.80[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2067916	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35044246	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35716055	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426191	0.80[JPT][hapmap]
rs7551797	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10924866	AHCTF1	Cis_1M	lymphoblastoid	RTeQTL
rs10924866	NLRP3	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247055400-247089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:247057800-247085400	Weak transcription	Pancreas	Pancrea
3	chr1:247061200-247093000	Weak transcription	Fetal Brain Male	brain
4	chr1:247065600-247088800	Weak transcription	Small Intestine	intestine
5	chr1:247069400-247087000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:247069600-247093400	Weak transcription	Colonic Mucosa	Colon
7	chr1:247069600-247093400	Weak transcription	Esophagus	oesophagus
8	chr1:247069800-247087000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:247069800-247087000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:247069800-247093800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:247070000-247093600	Weak transcription	Aorta	Aorta
12	chr1:247070400-247087000	Weak transcription	Lung	lung
13	chr1:247070800-247092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:247071000-247093400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:247071200-247087000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:247072200-247088800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:247073400-247086800	Weak transcription	Spleen	Spleen
18	chr1:247073600-247089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:247074200-247093400	Weak transcription	NHLF	lung
20	chr1:247075000-247085400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:247075600-247088800	Weak transcription	Fetal Stomach	stomach
22	chr1:247078400-247093600	Weak transcription	Fetal Kidney	kidney
23	chr1:247078600-247087000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:247078600-247089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:247078600-247093400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:247078800-247085400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:247078800-247093400	Weak transcription	Fetal Intestine Large	intestine
28	chr1:247079200-247089000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:247080200-247085000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:247080400-247093400	Weak transcription	Stomach Mucosa	stomach
31	chr1:247080600-247085200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:247080800-247085400	Weak transcription	Placenta	Placenta
33	chr1:247080800-247085400	Weak transcription	Left Ventricle	heart
34	chr1:247080800-247085400	Weak transcription	Psoas Muscle	Psoas
35	chr1:247080800-247086800	Weak transcription	Fetal Heart	heart
36	chr1:247080800-247086800	Weak transcription	Fetal Lung	lung
37	chr1:247080800-247087000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:247080800-247087000	Weak transcription	Gastric	stomach
39	chr1:247080800-247088400	Weak transcription	Fetal Brain Female	brain
40	chr1:247080800-247088800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:247080800-247089800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:247080800-247092000	Weak transcription	NHEK	skin
43	chr1:247081000-247085000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:247081000-247086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:247081000-247086800	Weak transcription	Brain Angular Gyrus	brain
46	chr1:247081000-247086800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:247081000-247086800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:247081000-247087000	Weak transcription	Brain Anterior Caudate	brain
49	chr1:247081000-247087000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:247081000-247088800	Weak transcription	H1 Cell Line	embryonic stem cell

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