Variant report

Variant	rs17399402
Chromosome Location	chr1:45822440-45822441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45476699..45479087-chr1:45821651..45824622,2	MCF-7	breast:
2	chr1:45820483..45822752-chr1:45823249..45826098,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUTYH-2	chr1:45821127-45822970	predAs_engstrom06_AK128017_1

Variant related genes	Relation type
ENSG00000238945	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3219474	1.00[AFR][1000 genomes]
rs3219486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45807200-45825800	Weak transcription	Small Intestine	intestine
2	chr1:45808800-45825600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:45810600-45825600	Weak transcription	Fetal Kidney	kidney
4	chr1:45811200-45825600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:45811200-45825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:45811200-45825600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:45811400-45825800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:45811400-45825800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:45811600-45825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:45812000-45826000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:45812200-45825800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:45812400-45825600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:45812400-45825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:45812600-45825600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:45812600-45825800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:45812600-45825800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:45812600-45826400	Weak transcription	Colonic Mucosa	Colon
18	chr1:45812800-45824400	Weak transcription	Gastric	stomach
19	chr1:45812800-45825600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:45812800-45825800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:45812800-45835800	Weak transcription	Thymus	Thymus
22	chr1:45813000-45825800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:45813200-45825800	Weak transcription	Spleen	Spleen
24	chr1:45813800-45825400	Weak transcription	Fetal Stomach	stomach
25	chr1:45815200-45825600	Weak transcription	Fetal Lung	lung
26	chr1:45815200-45825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:45815200-45825800	Weak transcription	Right Atrium	heart
28	chr1:45815400-45825600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:45815400-45825600	Weak transcription	GM12878-XiMat	blood
30	chr1:45815400-45825800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:45815400-45826000	Weak transcription	Esophagus	oesophagus
32	chr1:45815400-45826000	Weak transcription	Left Ventricle	heart
33	chr1:45815600-45825600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:45816400-45825800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:45817400-45825800	Weak transcription	Ovary	ovary
36	chr1:45817600-45825800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:45818000-45825600	Weak transcription	Primary B cells from cord blood	blood
38	chr1:45819600-45825800	Weak transcription	Brain Substantia Nigra	brain
39	chr1:45819800-45825400	Weak transcription	Placenta	Placenta
40	chr1:45819800-45825600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:45819800-45825800	Weak transcription	Fetal Intestine Large	intestine
42	chr1:45819800-45825800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:45820000-45825600	Weak transcription	Liver	Liver
44	chr1:45820000-45825800	Weak transcription	Brain Angular Gyrus	brain
45	chr1:45820600-45822600	Enhancers	HepG2	liver
46	chr1:45820800-45825600	Weak transcription	Fetal Intestine Small	intestine
47	chr1:45821000-45822600	Enhancers	Hela-S3	cervix
48	chr1:45821000-45823200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr1:45821200-45822800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:45821200-45825600	Weak transcription	Primary B cells from peripheral blood	blood

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