Variant report

Variant	rs56311849
Chromosome Location	chr2:38764039-38764040
allele	C/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	JUN	chr2:38763997-38764195	HepG2	liver:	n/a	chr2:38764040-38764053
2	CTCF	chr2:38762845-38764196	A549	lung:	n/a	chr2:38763399-38763417 chr2:38763400-38763416 chr2:38763402-38763415 chr2:38763404-38763414 chr2:38763402-38763415 chr2:38763399-38763412 chr2:38763402-38763411 chr2:38763401-38763422
3	JUND	chr2:38763912-38764140	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:38761973-38764297	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38739504..38742255-chr2:38763977..38765619,2	K562	blood:
2	chr2:38763564..38765964-chr2:38977063..38979087,3	K562	blood:
3	chr2:38603492..38605404-chr2:38761964..38764089,2	K562	blood:
4	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
5	chr2:38763564..38765964-chr2:38977063..38979194,4	K562	blood:

Variant related genes	Relation type
ENSG00000271443	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000119787	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10164547	0.94[ASN][1000 genomes]
rs12105827	0.82[EUR][1000 genomes]
rs13030122	0.85[ASN][1000 genomes]
rs17421399	0.82[EUR][1000 genomes]
rs17493321	0.82[EUR][1000 genomes]
rs34218951	0.81[EUR][1000 genomes]
rs6721860	0.81[EUR][1000 genomes]
rs7571463	0.89[EUR][1000 genomes]
rs7574556	0.82[EUR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763400-38768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:38763600-38767200	Weak transcription	Esophagus	oesophagus
3	chr2:38763600-38767400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:38763600-38767600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:38763600-38767800	Weak transcription	Stomach Mucosa	stomach
6	chr2:38763600-38768200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:38763600-38768200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:38763600-38768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:38763600-38768800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:38763600-38769000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:38763600-38770200	Weak transcription	HSMMtube	muscle
12	chr2:38763600-38771000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:38763800-38764200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:38763800-38764200	Enhancers	Liver	Liver
16	chr2:38763800-38764600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:38763800-38764800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:38763800-38765000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:38763800-38765200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:38763800-38765200	Weak transcription	NH-A	brain
21	chr2:38763800-38765400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:38763800-38767200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:38763800-38767400	Weak transcription	Fetal Brain Female	brain
24	chr2:38763800-38767600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:38763800-38767600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:38763800-38767600	Weak transcription	Fetal Brain Male	brain
27	chr2:38763800-38767600	Weak transcription	Fetal Intestine Large	intestine
28	chr2:38763800-38767600	Weak transcription	Fetal Intestine Small	intestine
29	chr2:38763800-38767600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:38763800-38767800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:38763800-38767800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:38763800-38767800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:38763800-38768400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:38763800-38768600	Weak transcription	Brain Anterior Caudate	brain
35	chr2:38763800-38769000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:38763800-38769400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:38763800-38769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:38764000-38764200	Flanking Active TSS	A549	lung
40	chr2:38764000-38764200	Enhancers	HepG2	liver
41	chr2:38764000-38767400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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