Variant report

Variant	rs10924985
Chromosome Location	chr1:247487085-247487086
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	chr1:247479235..247481801-chr1:247485562..247488525,3	K562	blood:
2	chr1:247481131..247482896-chr1:247485976..247487995,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10754542	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10754544	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10924983	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10924989	0.89[ASN][1000 genomes]
rs11578583	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1192830	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1192831	0.90[ASN][1000 genomes]
rs1192832	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12035515	0.84[ASN][1000 genomes]
rs1204493	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1341173	0.80[AMR][1000 genomes]
rs1616299	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771929	0.80[AMR][1000 genomes]
rs1771943	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771948	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1778544	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1778546	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1778549	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153631	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2799540	0.80[AMR][1000 genomes]
rs3850824	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4320815	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925532	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925533	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925534	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925615	0.92[ASN][1000 genomes]
rs4925621	0.84[ASN][1000 genomes]
rs56037169	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56399534	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674425	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692645	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418221	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528202	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540329	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552292	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875883	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426180	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426181	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426182	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426233	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9725334	0.85[EUR][1000 genomes];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10924985	ZNF496	cis	Esophagus Muscularis	GTEx
rs10924985	EDIL3	trans	lymphoblastoid	RTeQTL
rs10924985	ZNF496	cis	lung	GTEx
rs10924985	ZNF496	cis	Nerve Tibial	GTEx
rs10924985	ZNF496	cis	Thyroid	GTEx

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	chr1:247461200-247488200	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	chr1:247479600-247487800	Strong transcription	Fetal Lung	lung
22	chr1:247479800-247493000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:247480000-247493600	Weak transcription	NHDF-Ad	bronchial
24	chr1:247482000-247492600	Strong transcription	Liver	Liver
25	chr1:247482200-247488600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:247482400-247493600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:247482600-247493400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:247482600-247493400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:247482800-247487400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:247482800-247487400	Strong transcription	Fetal Intestine Large	intestine
31	chr1:247482800-247492400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:247482800-247493400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:247482800-247493400	Strong transcription	A549	lung
34	chr1:247482800-247493600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:247483000-247488200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:247483000-247488200	Strong transcription	Left Ventricle	heart
37	chr1:247483000-247493200	Strong transcription	Brain Germinal Matrix	brain
38	chr1:247483000-247493200	Strong transcription	Fetal Brain Female	brain
39	chr1:247483200-247488400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:247483200-247489200	Strong transcription	Hela-S3	cervix
41	chr1:247483400-247487800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:247483400-247488200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:247483400-247488600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:247483400-247489000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:247483400-247490000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:247483400-247493000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:247483400-247493200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:247483600-247488200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:247483600-247488400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:247484200-247487200	Strong transcription	Lung	lung

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