Variant report

Variant	rs62341097
Chromosome Location	chr4:174094940-174094941
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	chr4:174094710-174095011	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:174094706..174097585-chr4:174104711..174106711,3	MCF-7	breast:
2	chr4:174094346..174096240-chr4:174110007..174112423,2	K562	blood:
3	chr4:174088223..174092682-chr4:174092972..174099857,11	MCF-7	breast:
4	chr4:174091292..174097320-chr4:174098048..174101316,8	K562	blood:

Variant related genes	Relation type
ENSG00000245213	TF binding region
ENSG00000109586	Chromatin interaction
ENSG00000245213	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs34098993	0.82[ASN][1000 genomes]
rs35794567	0.82[ASN][1000 genomes]
rs71609815	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71609816	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[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	esv1793960	chr4:174090004-174102397	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1801469	chr4:174090004-174102397	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Neuritic plaque	25188341	GWAS catalog

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091600-174095000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
3	chr4:174091800-174104000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr4:174092000-174095000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:174092000-174096800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:174092000-174098600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:174092200-174096200	Enhancers	Duodenum Mucosa	Duodenum
8	chr4:174092200-174096400	Enhancers	Stomach Mucosa	stomach
9	chr4:174092200-174098800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:174092200-174099000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr4:174092200-174099000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr4:174092400-174100400	Weak transcription	Hela-S3	cervix
13	chr4:174092600-174095000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:174092600-174095000	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:174092600-174095000	Weak transcription	Fetal Kidney	kidney
16	chr4:174092600-174095400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:174092600-174096800	Enhancers	Primary hematopoietic stem cells	blood
18	chr4:174092600-174097800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:174092600-174099200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:174092600-174099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:174092600-174102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:174092800-174095000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:174092800-174095000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:174092800-174095000	Weak transcription	Fetal Intestine Small	intestine
25	chr4:174092800-174095000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:174092800-174095000	Enhancers	K562	blood
27	chr4:174092800-174095200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:174092800-174095400	Weak transcription	Fetal Lung	lung
29	chr4:174092800-174095600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:174092800-174096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:174092800-174096000	Enhancers	A549	lung
32	chr4:174092800-174096200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:174092800-174098600	Enhancers	Fetal Thymus	thymus
34	chr4:174092800-174099200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr4:174092800-174099400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:174092800-174100400	Weak transcription	NHEK	skin
37	chr4:174092800-174101000	Weak transcription	HSMM	muscle
38	chr4:174092800-174103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:174092800-174103600	Weak transcription	Aorta	Aorta
40	chr4:174092800-174106000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:174092800-174109000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:174093000-174096800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr4:174093000-174102200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:174093400-174097600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr4:174093600-174095200	Weak transcription	Fetal Intestine Large	intestine
46	chr4:174093600-174097000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:174093600-174102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:174093600-174109800	Weak transcription	Gastric	stomach
49	chr4:174093800-174095400	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr4:174093800-174105000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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