Variant report

Variant	rs6660212
Chromosome Location	chr1:224619015-224619016
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:224618074-224619050	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr1:224618981-224619133	K562	blood:	n/a	n/a
3	POLR2A	chr1:224618157-224621611	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr1:224618140-224619026	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr1:224618040-224619024	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224369742..224372382-chr1:224618245..224620019,2	MCF-7	breast:
2	chr1:224617651..224619446-chr1:224625035..224626931,2	MCF-7	breast:
3	chr1:224031722..224035110-chr1:224617781..224620783,3	K562	blood:
4	chr1:224543781..224546462-chr1:224616960..224621011,5	K562	blood:

No data

Variant related genes	Relation type
CNIH3	TF binding region
ENSG00000143514	Chromatin interaction
ENSG00000143753	Chromatin interaction
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10733025	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10799575	0.87[AFR][1000 genomes]
rs12078630	0.85[AMR][1000 genomes]
rs1573088	0.91[AFR][1000 genomes]
rs2405045	0.85[AMR][1000 genomes]
rs2405048	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2897051	0.85[AMR][1000 genomes]
rs4233237	0.85[AMR][1000 genomes]
rs6426119	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6426124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6426127	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6675269	0.85[AMR][1000 genomes]
rs6687870	0.85[AMR][1000 genomes]
rs6692855	0.85[AMR][1000 genomes]
rs6694310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7538718	0.85[AMR][1000 genomes]
rs7544512	0.87[AFR][1000 genomes]
rs9970442	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224608400-224620800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:224612000-224619400	Weak transcription	Stomach Mucosa	stomach
3	chr1:224612200-224619200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:224612400-224619200	Weak transcription	Right Ventricle	heart
5	chr1:224612400-224620000	Weak transcription	Ovary	ovary
6	chr1:224612400-224620400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:224612400-224620400	Weak transcription	Esophagus	oesophagus
8	chr1:224612400-224620400	Weak transcription	Pancreas	Pancrea
9	chr1:224612400-224620600	Weak transcription	Spleen	Spleen
10	chr1:224613000-224620400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:224613000-224620400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:224616800-224620200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:224616800-224620800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:224617000-224619200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:224617000-224619200	Weak transcription	Left Ventricle	heart
16	chr1:224617000-224619400	Weak transcription	Fetal Stomach	stomach
17	chr1:224617000-224620400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:224617000-224620400	Weak transcription	Gastric	stomach
19	chr1:224617000-224620400	Weak transcription	Lung	lung
20	chr1:224617200-224619400	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:224617200-224620200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:224617400-224619400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:224617400-224619400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:224617400-224619400	Genic enhancers	Fetal Kidney	kidney
25	chr1:224617600-224619200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:224617600-224619200	Enhancers	Colon Smooth Muscle	Colon
27	chr1:224617600-224619400	Enhancers	Adipose Nuclei	Adipose
28	chr1:224617600-224619400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:224617600-224619400	Transcr. at gene 5' and 3'	NH-A	brain
30	chr1:224617600-224620000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:224617600-224621000	Transcr. at gene 5' and 3'	K562	blood
32	chr1:224617600-224621200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:224617800-224619200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:224617800-224619200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:224617800-224619200	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:224617800-224621000	Flanking Active TSS	HUVEC	blood vessel
37	chr1:224618000-224619200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:224618000-224619200	Enhancers	Brain Substantia Nigra	brain
39	chr1:224618000-224620600	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:224618000-224621200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr1:224618200-224619200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:224618200-224619200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:224618200-224619200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:224618200-224619200	Enhancers	Brain Hippocampus Middle	brain
45	chr1:224618200-224619600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:224618200-224619800	Enhancers	Fetal Intestine Small	intestine
47	chr1:224618400-224619200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
48	chr1:224618400-224619200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr1:224618400-224619200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr1:224618400-224619400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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