Variant report

Variant	rs1192830
Chromosome Location	chr1:247455370-247455371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr1:247455238-247455377	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247455319..247457914-chr1:247494277..247496616,2	MCF-7	breast:
2	chr1:247453061..247455721-chr1:247491943..247494376,2	K562	blood:

Variant related genes	Relation type
ENSG00000202079	TF binding region
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10754542	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10754544	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs10924983	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10924985	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11578583	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1192832	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]
rs12035515	0.84[ASN][1000 genomes]
rs1204493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341173	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1614597	0.82[CEU][hapmap]
rs1616299	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771929	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771940	0.80[CEU][hapmap]
rs1771943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771948	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778544	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778546	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778549	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153631	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2799540	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3850824	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4320815	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925532	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925533	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925534	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4925621	0.82[ASN][1000 genomes]
rs56037169	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56399534	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674425	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74163745	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7418221	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7528202	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540329	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552292	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875883	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426180	0.85[CEU][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426181	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426233	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9725334	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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
rs1192830	ZNF496	cis	lung	GTEx
rs1192830	ZNF496	cis	Thyroid	GTEx
rs1192830	EDIL3	trans	lymphoblastoid	RTeQTL
rs1192830	ZNF496	cis	Nerve Tibial	GTEx
rs1192830	ZNF496	cis	Esophagus Muscularis	GTEx
rs1192830	ZNF496	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247436800-247457000	Weak transcription	HSMMtube	muscle
2	chr1:247445600-247455400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:247452400-247455600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
11	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:247452800-247455400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:247452800-247455600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:247453000-247456200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
17	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:247453200-247460400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
22	chr1:247454400-247455600	Enhancers	Thymus	Thymus
23	chr1:247454400-247457600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
25	chr1:247454600-247458000	Enhancers	K562	blood
26	chr1:247454800-247458400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:247454800-247458400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:247454800-247459800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:247455000-247455800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:247455000-247457800	Enhancers	Placenta	Placenta
31	chr1:247455000-247458400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:247455000-247460000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
34	chr1:247455200-247455800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr1:247455200-247455800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:247455200-247455800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr1:247455200-247457800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:247455200-247460000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:247455200-247460200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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