Variant report

Variant	rs9660023
Chromosome Location	chr1:67389801-67389802
allele	A/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	POLR2A	chr1:67389704-67389806	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:67389594-67389895	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:67388273-67391644	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:67389650-67392200	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr1:67389481-67391986	IMR90	lung:	n/a	n/a
6	ELF1	chr1:67389683-67390275	K562	blood:	n/a	n/a
7	POLR2A	chr1:67389625-67391999	HEK293	kidney:	n/a	n/a
8	POLR2A	chr1:67387931-67391585	MCF10A-Er-Src	breast:	n/a	n/a
9	SMARCB1	chr1:67389682-67391509	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:67388646-67389864	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67389047..67393171-chr1:67393255..67399137,11	MCF-7	breast:
2	chr1:67385997..67392679-chr1:67394416..67400305,9	MCF-7	breast:

Variant related genes	Relation type
MIER1	TF binding region
ENSG00000198160	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11208970	0.81[AMR][1000 genomes]
rs11208975	0.90[AMR][1000 genomes]
rs12061039	0.90[AMR][1000 genomes]
rs12083687	0.81[AMR][1000 genomes]
rs12090768	0.90[AMR][1000 genomes]
rs12091598	0.81[AMR][1000 genomes]
rs17097309	0.81[AMR][1000 genomes]
rs2104414	0.81[AMR][1000 genomes]
rs7528178	0.90[AMR][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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv871720	chr1:67357596-67435161	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv947266	chr1:67358868-67399427	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3448405	chr1:67360980-67393830	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67388600-67392400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr1:67388800-67390000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:67388800-67390000	Flanking Active TSS	Fetal Brain Female	brain
4	chr1:67388800-67390000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:67388800-67390000	Flanking Active TSS	Dnd41	blood
6	chr1:67388800-67392800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:67389000-67390000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:67389000-67390000	Enhancers	Stomach Mucosa	stomach
9	chr1:67389000-67391600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:67389000-67392000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:67389200-67390000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:67389200-67390000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr1:67389200-67390000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:67389200-67390000	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr1:67389200-67390000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:67389200-67390000	Enhancers	Gastric	stomach
17	chr1:67389200-67390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:67389200-67390200	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr1:67389200-67390200	Enhancers	Spleen	Spleen
20	chr1:67389200-67390600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:67389200-67391000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:67389200-67392000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:67389200-67392000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:67389200-67392200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:67389400-67390000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:67389400-67390000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr1:67389400-67390000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:67389400-67390000	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr1:67389400-67390000	Flanking Active TSS	HUVEC	blood vessel
30	chr1:67389400-67390200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr1:67389400-67390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:67389400-67390200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:67389400-67391200	Active TSS	Colonic Mucosa	Colon
34	chr1:67389400-67392000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:67389400-67392000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:67389600-67390000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:67389600-67390000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:67389600-67390000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:67389600-67390000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:67389600-67390000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:67389600-67390000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr1:67389600-67390000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr1:67389600-67390000	Flanking Active TSS	Liver	Liver
44	chr1:67389600-67390000	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr1:67389600-67390000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:67389600-67390000	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr1:67389600-67390000	Flanking Active TSS	Placenta	Placenta
48	chr1:67389600-67390000	Flanking Active TSS	Fetal Thymus	thymus
49	chr1:67389600-67390000	Flanking Active TSS	Pancreas	Pancrea
50	chr1:67389600-67390000	Active TSS	HepG2	liver

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