Variant report

Variant	rs6690864
Chromosome Location	chr1:247490707-247490708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247456296..247458047-chr1:247490288..247491803,2	K562	blood:
2	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10754545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1192833	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs12023326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12023478	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12026978	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12027522	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12034916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035371	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12035515	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12047860	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404914	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17664745	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1771925	0.80[CEU][hapmap]
rs3850825	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs56013900	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56322048	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56335231	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56366903	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56396334	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58522562	0.83[ASN][1000 genomes]
rs6426239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697861	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7522071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	esv1848384	chr1:247485654-247495666	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6690864	NLRP3	cis	cerebellum	SCAN
rs6690864	ZNF496	Cis_1M	lymphoblastoid	RTeQTL
rs6690864	ZNF496	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
2	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:247464800-247493400	Strong transcription	Fetal Stomach	stomach
9	chr1:247465200-247493400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:247467600-247493800	Weak transcription	Stomach Mucosa	stomach
11	chr1:247468400-247494000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:247469000-247493600	Weak transcription	Psoas Muscle	Psoas
13	chr1:247469400-247493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:247471800-247493400	Weak transcription	Fetal Heart	heart
15	chr1:247472800-247493400	Weak transcription	Small Intestine	intestine
16	chr1:247476600-247491400	Strong transcription	Dnd41	blood
17	chr1:247476600-247494000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:247479800-247493000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:247480000-247493600	Weak transcription	NHDF-Ad	bronchial
20	chr1:247482000-247492600	Strong transcription	Liver	Liver
21	chr1:247482400-247493600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:247482600-247493400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:247482600-247493400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:247482800-247492400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:247482800-247493400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:247482800-247493400	Strong transcription	A549	lung
27	chr1:247482800-247493600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:247483000-247493200	Strong transcription	Brain Germinal Matrix	brain
29	chr1:247483000-247493200	Strong transcription	Fetal Brain Female	brain
30	chr1:247483400-247493000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:247483400-247493200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:247484600-247493400	Weak transcription	Ovary	ovary
33	chr1:247485600-247491400	Weak transcription	Fetal Brain Male	brain
34	chr1:247485800-247491400	Weak transcription	Fetal Kidney	kidney
35	chr1:247486000-247491800	Weak transcription	Pancreas	Pancrea
36	chr1:247486400-247491400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:247486400-247491400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:247486400-247491800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:247486400-247491800	Weak transcription	Esophagus	oesophagus
40	chr1:247486400-247493400	Strong transcription	NH-A	brain
41	chr1:247486600-247491200	Weak transcription	Colonic Mucosa	Colon
42	chr1:247486600-247491200	Weak transcription	HMEC	breast
43	chr1:247486600-247491400	Weak transcription	Aorta	Aorta
44	chr1:247486600-247491600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr1:247486600-247491800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:247486600-247491800	Weak transcription	Spleen	Spleen
47	chr1:247486800-247491200	Weak transcription	NHLF	lung
48	chr1:247486800-247491600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:247486800-247491600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:247486800-247491600	Weak transcription	Right Ventricle	heart

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