Variant report

Variant	rs1006538
Chromosome Location	chr2:11905317-11905318
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	EP300	chr2:11904265-11906727	SK-N-SH	brain:	n/a	chr2:11904815-11904829
2	MXI1	chr2:11904319-11905508	SK-N-SH	brain:	n/a	chr2:11904978-11904987
3	GATA2	chr2:11904452-11905355	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr2:11905078-11905363	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11887777..11889810-chr2:11903193..11905347,2	K562	blood:
2	chr2:11902752..11905515-chr2:11914841..11917001,2	K562	blood:
3	chr2:11901357..11903016-chr2:11903554..11905723,2	MCF-7	breast:

Variant related genes	Relation type
MIR548S	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10169802	0.91[ASN][1000 genomes]
rs10191952	0.80[JPT][hapmap]
rs10191977	0.80[JPT][hapmap]
rs10192566	0.91[ASN][1000 genomes]
rs10205312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10205400	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10207506	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10208679	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10209969	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11676086	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11693809	0.91[ASN][1000 genomes]
rs11897144	0.94[ASN][1000 genomes]
rs13407101	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13409154	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13412852	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1469952	0.92[ASN][1000 genomes]
rs17603420	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2099597	0.82[ASN][1000 genomes]
rs2278513	0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2358041	0.98[ASN][1000 genomes]
rs2358042	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2358126	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4076055	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4129757	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4315495	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62113306	0.88[ASN][1000 genomes]
rs6717910	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6731096	0.88[ASN][1000 genomes]
rs6757892	0.83[ASN][1000 genomes]
rs72773994	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7561070	0.83[ASN][1000 genomes]
rs7595221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7607755	0.83[ASN][1000 genomes]
rs873358	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs893342	0.99[ASN][1000 genomes]
rs893349	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11888400-11916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:11890400-11906400	Weak transcription	Fetal Brain Male	brain
3	chr2:11890600-11905800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:11893800-11906400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:11895000-11905400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:11895000-11905800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:11895000-11905800	Weak transcription	HSMMtube	muscle
8	chr2:11895000-11905800	Weak transcription	NH-A	brain
9	chr2:11895000-11905800	Weak transcription	Osteobl	bone
10	chr2:11895000-11906000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:11895000-11906200	Weak transcription	HSMM	muscle
12	chr2:11895000-11907000	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:11895000-11918200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:11895600-11905600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:11895800-11905600	Weak transcription	NHDF-Ad	bronchial
16	chr2:11895800-11905800	Weak transcription	Spleen	Spleen
17	chr2:11897400-11905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:11897600-11909000	Weak transcription	Psoas Muscle	Psoas
19	chr2:11898600-11906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:11899200-11905400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:11899200-11906000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:11899200-11911200	Weak transcription	Small Intestine	intestine
23	chr2:11899400-11905600	Weak transcription	Placenta	Placenta
24	chr2:11900600-11908800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:11900600-11918000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:11900800-11912200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:11901000-11905400	Weak transcription	Brain Germinal Matrix	brain
28	chr2:11901000-11905400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:11901200-11909000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:11901200-11915000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:11901400-11905600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:11901600-11905800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:11901600-11914200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:11901800-11914000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:11901800-11918600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:11902000-11905400	Enhancers	Fetal Heart	heart
37	chr2:11902000-11905800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:11902200-11905600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:11902200-11905600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:11902200-11905800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:11902200-11906600	Weak transcription	Fetal Kidney	kidney
42	chr2:11902200-11913800	Strong transcription	NHLF	lung
43	chr2:11902800-11905400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:11902800-11905400	Enhancers	Right Atrium	heart
45	chr2:11902800-11906000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:11902800-11906000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:11902800-11912200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:11902800-11912400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:11902800-11913800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:11903000-11908400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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