Variant report

Variant	rs1192832
Chromosome Location	chr1:247455896-247455897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247455319..247457914-chr1:247494277..247496616,2	MCF-7	breast:
2	chr1:247455456..247457066-chr1:247457256..247459121,2	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction
ENSG00000202079	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10754542	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10754544	0.84[EUR][1000 genomes]
rs10924983	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10924985	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10924989	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11578583	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1192830	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12035515	0.84[ASN][1000 genomes]
rs1204493	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1341173	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1616299	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1771929	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1771943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1771948	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778544	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778546	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778549	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153631	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799540	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3850824	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4320815	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925532	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925533	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925534	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4925621	0.81[ASN][1000 genomes]
rs56037169	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56399534	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674425	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6692645	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74163745	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7418221	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7528202	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540329	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552292	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875883	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426180	0.80[CEU][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9426181	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426182	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426233	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9725334	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	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
4	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
5	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1192832	ZNF496	cis	Thyroid	GTEx
rs1192832	EDIL3	trans	lymphoblastoid	RTeQTL
rs1192832	ZNF496	cis	lung	GTEx
rs1192832	ZNF496	cis	Skin Sun Exposed Lower leg	GTEx
rs1192832	ZNF496	cis	Nerve Tibial	GTEx
rs1192832	ZNF496	cis	Esophagus Muscularis	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247436800-247457000	Weak transcription	HSMMtube	muscle
2	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
3	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:247453000-247456200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
13	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:247453200-247460400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
17	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
18	chr1:247454400-247457600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
20	chr1:247454600-247458000	Enhancers	K562	blood
21	chr1:247454800-247458400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:247454800-247458400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:247454800-247459800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:247455000-247457800	Enhancers	Placenta	Placenta
25	chr1:247455000-247458400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:247455000-247460000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
28	chr1:247455200-247457800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:247455200-247460000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:247455200-247460200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr1:247455400-247456800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:247455400-247459800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:247455400-247461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:247455600-247456200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:247455600-247457000	Weak transcription	Thymus	Thymus
38	chr1:247455600-247457800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:247455600-247459000	Enhancers	NH-A	brain
40	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
41	chr1:247455800-247456200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:247455800-247456600	Enhancers	Fetal Heart	heart
43	chr1:247455800-247459000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:247455800-247459800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:247455800-247460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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