Variant report

Variant	rs17394244
Chromosome Location	chr1:79131132-79131133
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	POLR2A	chr1:79130303-79131185	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:79130394-79132133	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:79130051-79132086	GM19193	blood:	n/a	n/a
4	POLR2A	chr1:79130391-79131266	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:79130103-79132411	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:79130817-79131199	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:79130326-79131278	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:79130464-79131292	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:79130150-79132433	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:79130036-79133193	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000238015	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10873993	1.00[ASN][1000 genomes]
rs10873994	1.00[ASN][1000 genomes]
rs11162526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11162543	1.00[ASN][1000 genomes]
rs12066013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081949	1.00[ASN][1000 genomes]
rs1628313	1.00[ASN][1000 genomes]
rs17394028	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1751524	1.00[ASN][1000 genomes]
rs55802282	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs60222720	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673963	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74092102	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7526675	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7536070	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79117000-79132800	Weak transcription	Fetal Brain Male	brain
2	chr1:79117400-79131200	Weak transcription	HSMM	muscle
3	chr1:79117400-79144000	Weak transcription	Esophagus	oesophagus
4	chr1:79117400-79144000	Weak transcription	Spleen	Spleen
5	chr1:79117600-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:79119800-79132600	Weak transcription	Right Ventricle	heart
7	chr1:79124800-79134000	Weak transcription	NHDF-Ad	bronchial
8	chr1:79125400-79133000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:79126200-79131200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:79126400-79138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:79126600-79148000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:79128600-79131400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:79129000-79132800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:79129000-79138200	Weak transcription	Lung	lung
15	chr1:79129200-79132600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:79129200-79143800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:79129400-79131200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:79129400-79131200	Weak transcription	HSMMtube	muscle
19	chr1:79129400-79132000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:79129400-79132000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:79129400-79132200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:79129400-79132200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:79129400-79133000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:79129400-79133400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:79129400-79135800	Weak transcription	Left Ventricle	heart
26	chr1:79129400-79137600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:79129400-79138200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:79129400-79138200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:79129400-79138600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:79129400-79139800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:79129400-79144000	Weak transcription	Ovary	ovary
32	chr1:79129600-79131400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:79129600-79131400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:79129600-79131400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:79129600-79141800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:79130000-79134200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:79130000-79141200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:79130200-79133400	Weak transcription	Liver	Liver
39	chr1:79130200-79135200	Weak transcription	Dnd41	blood
40	chr1:79130200-79141800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:79130400-79132200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:79130600-79132400	Weak transcription	Adipose Nuclei	Adipose
43	chr1:79130800-79132400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:79130800-79135200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:79130800-79135600	Weak transcription	GM12878-XiMat	blood
46	chr1:79130800-79144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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