Variant report

Variant	rs6426239
Chromosome Location	chr1:247486736-247486737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247479235..247481801-chr1:247485562..247488525,3	K562	blood:
2	chr1:247484997..247486937-chr1:247500462..247503140,2	K562	blood:
3	chr1:247481131..247482896-chr1:247485976..247487995,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10754545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192833	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.92[ASN][1000 genomes]
rs12023326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023478	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12026978	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12027522	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034916	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12034919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12035371	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12035515	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047860	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12048553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12404914	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17664745	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771925	0.80[CEU][hapmap]
rs3850825	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs56013900	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56322048	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56335231	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56366903	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56396334	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56740645	0.80[ASN][1000 genomes]
rs58522562	0.84[ASN][1000 genomes]
rs6690864	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];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7522071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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
rs6426239	ZNF496	Cis_1M	lymphoblastoid	RTeQTL
rs6426239	ZNF496	cis	cerebellum	SCAN
rs6426239	NLRP3	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:247462800-247488000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:247464800-247493400	Strong transcription	Fetal Stomach	stomach
11	chr1:247465200-247493400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:247467600-247493800	Weak transcription	Stomach Mucosa	stomach
13	chr1:247468400-247494000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:247469000-247493600	Weak transcription	Psoas Muscle	Psoas
15	chr1:247469400-247493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:247471800-247493400	Weak transcription	Fetal Heart	heart
17	chr1:247472800-247493400	Weak transcription	Small Intestine	intestine
18	chr1:247474000-247488200	Weak transcription	Gastric	stomach
19	chr1:247476600-247491400	Strong transcription	Dnd41	blood
20	chr1:247476600-247494000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:247478400-247486800	Strong transcription	K562	blood
22	chr1:247479600-247487800	Strong transcription	Fetal Lung	lung
23	chr1:247479800-247493000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:247480000-247493600	Weak transcription	NHDF-Ad	bronchial
25	chr1:247481800-247487000	Strong transcription	Placenta	Placenta
26	chr1:247482000-247492600	Strong transcription	Liver	Liver
27	chr1:247482200-247488600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:247482400-247493600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:247482600-247486800	Strong transcription	HSMM	muscle
30	chr1:247482600-247487000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:247482600-247493400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:247482600-247493400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:247482800-247486800	Strong transcription	Osteobl	bone
34	chr1:247482800-247487000	Strong transcription	Brain Hippocampus Middle	brain
35	chr1:247482800-247487000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:247482800-247487400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:247482800-247487400	Strong transcription	Fetal Intestine Large	intestine
38	chr1:247482800-247492400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:247482800-247493400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:247482800-247493400	Strong transcription	A549	lung
41	chr1:247482800-247493600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:247483000-247486800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:247483000-247487000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:247483000-247487000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:247483000-247487000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:247483000-247488200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:247483000-247488200	Strong transcription	Left Ventricle	heart
48	chr1:247483000-247493200	Strong transcription	Brain Germinal Matrix	brain
49	chr1:247483000-247493200	Strong transcription	Fetal Brain Female	brain
50	chr1:247483200-247488400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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