Variant report

Variant	rs41478448
Chromosome Location	chr11:68181621-68181622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:68180693..68182317-chr11:68187178..68189389,2	MCF-7	breast:
2	chr11:68179782..68183196-chr11:68190274..68193170,4	MCF-7	breast:
3	chr11:68180583..68185146-chr11:68190126..68194877,4	K562	blood:
4	chr11:68179869..68181854-chr11:68189096..68191127,2	MCF-7	breast:
5	chr11:68037863..68040353-chr11:68181115..68182720,2	MCF-7	breast:
6	chr11:67981272..67983377-chr11:68179703..68181809,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171067	Chromatin interaction
ENSG00000110066	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1784235	0.86[ASN][1000 genomes]
rs2306862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472415	0.86[ASN][1000 genomes]
rs2508834	0.87[ASN][1000 genomes]
rs3736228	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3781586	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs475712	0.86[ASN][1000 genomes]
rs546803	0.87[ASN][1000 genomes]
rs56400711	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576118	0.88[ASN][1000 genomes]
rs583545	0.88[ASN][1000 genomes]
rs640569	0.88[ASN][1000 genomes]
rs6591339	0.86[ASN][1000 genomes]
rs667126	0.88[ASN][1000 genomes]
rs685095	0.81[ASN][1000 genomes]
rs689179	0.88[ASN][1000 genomes]
rs7102451	0.87[ASN][1000 genomes]
rs7106320	0.88[AMR][1000 genomes]
rs880610	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1039671	chr11:68120571-68206630	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv897861	chr11:68129606-68196830	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv469965	chr11:68140781-68217420	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv555285	chr11:68144283-68231240	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv468618	chr11:68171013-68231240	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41478448	CPT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68148600-68196800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:68157200-68196600	Weak transcription	NH-A	brain
3	chr11:68167800-68196600	Weak transcription	Fetal Brain Male	brain
4	chr11:68168400-68185000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:68168400-68189000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:68168600-68188800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:68168600-68188800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:68168600-68193600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:68168600-68195600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:68169000-68193600	Strong transcription	Fetal Intestine Small	intestine
11	chr11:68169400-68196600	Weak transcription	Right Atrium	heart
12	chr11:68169600-68188200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:68169600-68196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:68173000-68184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:68173000-68188400	Strong transcription	Dnd41	blood
16	chr11:68173400-68184200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:68173400-68187400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:68173800-68189000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:68174400-68192800	Strong transcription	Fetal Intestine Large	intestine
20	chr11:68174400-68195800	Weak transcription	Primary B cells from cord blood	blood
21	chr11:68174600-68196800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:68175400-68184800	Strong transcription	Fetal Lung	lung
23	chr11:68175600-68196000	Strong transcription	Brain Germinal Matrix	brain
24	chr11:68176000-68184800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:68176000-68210400	Strong transcription	HepG2	liver
26	chr11:68176200-68182800	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr11:68176200-68186400	Strong transcription	Pancreas	Pancrea
28	chr11:68177000-68182400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:68177000-68182800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:68177000-68184800	Strong transcription	NHEK	skin
31	chr11:68177000-68185000	Strong transcription	Primary T cells from cord blood	blood
32	chr11:68177200-68184800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr11:68177200-68184800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:68177200-68184800	Strong transcription	Fetal Brain Female	brain
35	chr11:68177200-68186000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:68177400-68182600	Genic enhancers	Fetal Muscle Leg	muscle
37	chr11:68177400-68182600	Strong transcription	Placenta	Placenta
38	chr11:68177400-68182800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:68177400-68183200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:68177400-68184600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:68177400-68184600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:68177400-68184800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:68177400-68184800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:68177400-68184800	Strong transcription	Aorta	Aorta
45	chr11:68177400-68184800	Strong transcription	Colon Smooth Muscle	Colon
46	chr11:68177400-68184800	Strong transcription	Rectal Smooth Muscle	rectum
47	chr11:68177400-68186600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:68177400-68187800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:68177600-68182600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr11:68177600-68184400	Strong transcription	H9 Cell Line	embryonic stem cell

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