Variant report

Variant	rs12048553
Chromosome Location	chr1:247477068-247477069
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	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
2	chr1:247456054..247458907-chr1:247476595..247478143,2	K562	blood:

Variant related genes	Relation type
ENSG00000202079	Chromatin interaction
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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];0.88[AMR][1000 genomes];0.95[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];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.95[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];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12023478	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12026978	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12027522	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12034916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12034919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12035371	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12035515	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047860	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12404914	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17664745	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56013900	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322048	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56335231	0.92[ASN][1000 genomes]
rs56366903	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56396334	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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];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]
rs6690864	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]
rs6697861	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7522071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12048553	ZNF496	cis	cerebellum	SCAN
rs12048553	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	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
5	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:247461600-247481000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:247462200-247480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:247462600-247479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:247462800-247488000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:247463000-247486200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:247463000-247486400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:247463200-247481000	Strong transcription	Left Ventricle	heart
21	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:247463400-247486000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:247463400-247486600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:247464600-247479600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:247464600-247486000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:247464800-247493400	Strong transcription	Fetal Stomach	stomach
27	chr1:247465200-247493400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:247466800-247485600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:247467600-247493800	Weak transcription	Stomach Mucosa	stomach
30	chr1:247468400-247494000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:247469000-247493600	Weak transcription	Psoas Muscle	Psoas
32	chr1:247469400-247478600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:247469400-247493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:247471200-247485600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:247471800-247478800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:247471800-247480400	Weak transcription	GM12878-XiMat	blood
37	chr1:247471800-247493400	Weak transcription	Fetal Heart	heart
38	chr1:247472400-247478600	Weak transcription	NHDF-Ad	bronchial
39	chr1:247472400-247483600	Weak transcription	Fetal Brain Male	brain
40	chr1:247472600-247484400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:247472800-247478600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:247472800-247478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:247472800-247482800	Weak transcription	Fetal Kidney	kidney
44	chr1:247472800-247493400	Weak transcription	Small Intestine	intestine
45	chr1:247473000-247485400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:247473000-247485600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:247473400-247480800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:247473400-247483600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:247473400-247484800	Weak transcription	Colonic Mucosa	Colon
50	chr1:247473400-247484800	Weak transcription	Rectal Smooth Muscle	rectum

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