Variant report

Variant	rs12409976
Chromosome Location	chr1:247323557-247323558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247317106..247320597-chr1:247321914..247325025,4	K562	blood:
2	chr1:247265787..247267676-chr1:247322422..247325392,2	MCF-7	breast:
3	chr1:247313509..247316825-chr1:247321741..247324519,3	MCF-7	breast:
4	chr1:247312926..247315544-chr1:247323490..247325492,2	K562	blood:
5	chr1:247312926..247314951-chr1:247323061..247325492,2	K562	blood:
6	chr1:247303971..247305642-chr1:247323338..247325925,2	K562	blood:
7	chr1:247323516..247325758-chr1:247334255..247337594,3	K562	blood:

Variant related genes	Relation type
ENSG00000196418	Chromatin interaction
ENSG00000188295	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10924929	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806327	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401877	1.00[ASN][1000 genomes]
rs12407350	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409513	1.00[ASN][1000 genomes]
rs12410313	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067086	1.00[ASN][1000 genomes]
rs4115690	1.00[ASN][1000 genomes]
rs4115691	1.00[ASN][1000 genomes]
rs41304032	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310581	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925528	1.00[ASN][1000 genomes]
rs4925765	1.00[ASN][1000 genomes]
rs4925766	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925767	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813682	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57418790	1.00[ASN][1000 genomes]
rs57793630	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59236805	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663210	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683966	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687789	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137962	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137971	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74152938	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516747	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551232	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924085	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	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
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
15	nsv873428	chr1:247226986-247346189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	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
17	nsv873432	chr1:247278707-247334323	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
18	nsv873433	chr1:247278707-247360368	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
19	nsv1005008	chr1:247285853-247339833	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
20	nsv535423	chr1:247285853-247339833	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
21	nsv873434	chr1:247319489-247360368	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
22	nsv945438	chr1:247320827-247323661	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12409976	ZNF124	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247301800-247333000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:247302000-247334200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:247303400-247324600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:247303600-247324600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr1:247304200-247324400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:247306600-247324000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr1:247306600-247324200	ZNF genes & repeats	GM12878-XiMat	blood
8	chr1:247309800-247324000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr1:247309800-247329000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:247310200-247324400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr1:247311000-247323800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr1:247312800-247324600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr1:247314200-247331000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr1:247314400-247323800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
15	chr1:247314800-247323800	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr1:247314800-247324200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:247315000-247325800	ZNF genes & repeats	Primary B cells from cord blood	blood
18	chr1:247315200-247325800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr1:247315800-247324800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
20	chr1:247315800-247325600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:247316400-247323800	ZNF genes & repeats	A549	lung
22	chr1:247316400-247324000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
23	chr1:247316400-247324000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:247316400-247324600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:247316400-247325600	ZNF genes & repeats	Liver	Liver
26	chr1:247316400-247325800	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr1:247316400-247325800	ZNF genes & repeats	Dnd41	blood
28	chr1:247316600-247323800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
29	chr1:247316600-247324600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
30	chr1:247316600-247325600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr1:247317000-247325600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
32	chr1:247318800-247323600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
33	chr1:247319400-247323600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:247319400-247324000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:247319400-247324200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
36	chr1:247319400-247324200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:247319400-247324800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:247319600-247323800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
39	chr1:247319600-247324000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:247319800-247323600	ZNF genes & repeats	Thymus	Thymus
41	chr1:247319800-247323800	ZNF genes & repeats	Psoas Muscle	Psoas
42	chr1:247319800-247323800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
43	chr1:247320000-247323600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:247320000-247324000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
45	chr1:247320800-247323800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:247320800-247324200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:247320800-247332800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:247321200-247323600	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr1:247321200-247324000	ZNF genes & repeats	Fetal Thymus	thymus
50	chr1:247321800-247323800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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