Variant report

Variant	rs2666501
Chromosome Location	chr1:62738471-62738472
allele	A/G
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	MXI1	chr1:62736526-62738487	SK-N-SH	brain:	n/a	n/a
2	EP300	chr1:62736081-62738530	SK-N-SH	brain:	n/a	chr1:62737919-62737928

Variant related genes	Relation type
KANK4	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10889317	0.87[EUR][1000 genomes]
rs11207949	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12037540	0.83[EUR][1000 genomes]
rs12044289	0.83[EUR][1000 genomes]
rs12082623	0.84[EUR][1000 genomes]
rs1325742	0.82[EUR][1000 genomes]
rs1886831	0.86[EUR][1000 genomes]
rs1886832	0.86[EUR][1000 genomes]
rs2666483	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2666502	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3844054	0.87[EUR][1000 genomes]
rs3850631	0.82[EUR][1000 genomes]
rs3895339	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4915811	0.86[EUR][1000 genomes]
rs6587965	0.87[EUR][1000 genomes]
rs6663943	0.82[EUR][1000 genomes]
rs7551135	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:62732400-62740000	Weak transcription	Liver	Liver
3	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:62734200-62750800	Weak transcription	Gastric	stomach
6	chr1:62735800-62740600	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:62736200-62739600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:62736400-62740400	Enhancers	Fetal Thymus	thymus
11	chr1:62736400-62741000	Strong transcription	HepG2	liver
12	chr1:62736800-62738800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:62736800-62739000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:62736800-62739000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:62736800-62739400	Enhancers	Primary T cells from cord blood	blood
16	chr1:62736800-62739600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:62736800-62739600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr1:62737000-62739200	Enhancers	Thymus	Thymus
19	chr1:62737000-62739400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:62737000-62740600	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr1:62737200-62738800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr1:62737400-62739000	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:62737600-62740600	Strong transcription	Fetal Intestine Small	intestine
24	chr1:62737600-62741800	Strong transcription	Placenta	Placenta
25	chr1:62737800-62739600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:62737800-62739600	Weak transcription	Lung	lung
27	chr1:62737800-62742600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
29	chr1:62738000-62739000	Weak transcription	Pancreas	Pancrea
30	chr1:62738000-62739400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:62738200-62738600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr1:62738200-62739800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
35	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:62738400-62738800	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:62738400-62739200	Weak transcription	Adipose Nuclei	Adipose
38	chr1:62738400-62739400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:62738400-62739400	Weak transcription	Fetal Lung	lung
40	chr1:62738400-62739400	Strong transcription	Fetal Stomach	stomach
41	chr1:62738400-62739400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:62738400-62740000	Weak transcription	Fetal Heart	heart
43	chr1:62738400-62740600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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