Variant report

Variant	rs2920842
Chromosome Location	chr2:55338488-55338489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
2	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
3	chr2:55275064..55278271-chr2:55336145..55339086,3	MCF-7	breast:
4	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12713288	0.91[GIH][hapmap]
rs6725139	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2920842	NRXN1	cis	cerebellum	SCAN
rs2920842	EFEMP1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55321600-55339400	Weak transcription	Thymus	Thymus
2	chr2:55325200-55340400	Weak transcription	Gastric	stomach
3	chr2:55327800-55338600	Weak transcription	Lung	lung
4	chr2:55327800-55338600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:55329000-55338600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:55329600-55342600	Weak transcription	NHEK	skin
7	chr2:55330600-55338600	Weak transcription	Aorta	Aorta
8	chr2:55331200-55339000	Weak transcription	Dnd41	blood
9	chr2:55331800-55338600	Weak transcription	Fetal Thymus	thymus
10	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:55332800-55338600	Enhancers	Osteobl	bone
12	chr2:55333000-55338600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:55333200-55338600	Enhancers	NHDF-Ad	bronchial
14	chr2:55333200-55338800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:55333600-55338600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:55334000-55338600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:55334000-55338600	Enhancers	Brain Hippocampus Middle	brain
18	chr2:55334200-55338600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:55334400-55340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:55334800-55338600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:55334800-55339400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr2:55335000-55339000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:55335200-55338600	Enhancers	HSMMtube	muscle
24	chr2:55335200-55339000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:55335400-55341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:55336200-55338600	Enhancers	K562	blood
27	chr2:55336600-55340000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:55336800-55338600	Weak transcription	Fetal Intestine Large	intestine
29	chr2:55336800-55338600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:55337000-55338600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:55337000-55338600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:55337000-55338600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:55337000-55338800	Weak transcription	Fetal Lung	lung
34	chr2:55337000-55339000	Weak transcription	Brain Germinal Matrix	brain
35	chr2:55337000-55339200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:55337000-55339400	Weak transcription	Fetal Brain Female	brain
37	chr2:55337000-55340000	Weak transcription	Fetal Kidney	kidney
38	chr2:55337200-55341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:55337400-55338600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:55337400-55338600	Weak transcription	Ovary	ovary
42	chr2:55337400-55338600	Weak transcription	Right Atrium	heart
43	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:55337400-55342800	Weak transcription	HMEC	breast
45	chr2:55337600-55338600	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:55337600-55338600	Weak transcription	Fetal Stomach	stomach
47	chr2:55337600-55338600	Enhancers	A549	lung
48	chr2:55337800-55339000	Weak transcription	Fetal Intestine Small	intestine
49	chr2:55338200-55338600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:55338200-55338600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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