Variant report

Variant	rs41220
Chromosome Location	chr14:71837479-71837480
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71786183..71790098-chr14:71837294..71842439,6	MCF-7	breast:
2	chr14:71829682..71831529-chr14:71835812..71838531,2	K562	blood:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2041331	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36531	0.87[ASN][1000 genomes]
rs36533	0.86[ASN][1000 genomes]
rs36534	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs40621	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs41216	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs41227	0.80[AFR][1000 genomes]
rs41228	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs718854	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8015579	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8019634	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1831401	chr14:71786411-71845264	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41220	L1CAM	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71806600-71838400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr14:71808800-71838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr14:71812200-71838800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:71820200-71838600	Weak transcription	Hela-S3	cervix
5	chr14:71820600-71838800	Weak transcription	Primary T cells from cord blood	blood
6	chr14:71828600-71838200	Weak transcription	Esophagus	oesophagus
7	chr14:71830000-71838200	Weak transcription	Fetal Intestine Small	intestine
8	chr14:71830600-71838600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:71830600-71838600	Weak transcription	Brain Angular Gyrus	brain
10	chr14:71831200-71838600	Weak transcription	HSMM	muscle
11	chr14:71831200-71838800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr14:71831400-71838200	Weak transcription	Osteobl	bone
13	chr14:71831400-71838800	Weak transcription	HSMMtube	muscle
14	chr14:71831600-71838400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr14:71831600-71838800	Weak transcription	Fetal Lung	lung
16	chr14:71831800-71838800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:71831800-71840600	Weak transcription	Spleen	Spleen
18	chr14:71832200-71837800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:71832200-71838400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:71832200-71843800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:71832400-71838200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr14:71832400-71838600	Weak transcription	NH-A	brain
23	chr14:71832600-71838000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr14:71832800-71837800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr14:71832800-71838600	Weak transcription	NHLF	lung
26	chr14:71833200-71838600	Weak transcription	Fetal Heart	heart
27	chr14:71833200-71838600	Weak transcription	HepG2	liver
28	chr14:71833200-71838600	Weak transcription	K562	blood
29	chr14:71833200-71843800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:71833600-71838800	Weak transcription	Primary B cells from cord blood	blood
31	chr14:71833600-71840000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:71833800-71838800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:71836600-71838400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:71836600-71840400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:71837000-71837600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr14:71837200-71837600	Enhancers	Primary B cells from peripheral blood	blood
37	chr14:71837200-71838400	Enhancers	NHEK	skin
38	chr14:71837200-71838800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:71837200-71839600	Enhancers	GM12878-XiMat	blood
40	chr14:71837200-71840600	Enhancers	Stomach Mucosa	stomach
41	chr14:71837400-71837600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr14:71837400-71837600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr14:71837400-71838400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr14:71837400-71838400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr14:71837400-71838400	Enhancers	Pancreas	Pancrea
46	chr14:71837400-71838600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr14:71837400-71838600	Enhancers	HMEC	breast
48	chr14:71837400-71839600	Enhancers	Small Intestine	intestine
49	chr14:71837400-71841600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr14:71837400-71855800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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