Variant report

Variant	rs641378
Chromosome Location	chr11:63869493-63869494
allele	C/T
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	FOXP2	chr11:63869390-63869906	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr11:63869463-63869824	SK-N-MC	brain:	n/a	n/a
3	TCF12	chr11:63869275-63869962	SK-N-SH	brain:	n/a	n/a
4	EP300	chr11:63869468-63869795	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr11:63869447-63869784	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr11:63867726-63870988	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr11:63869477-63869771	SK-N-SH_RA	brain:	n/a	chr11:63869693-63869706

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63857132..63859776-chr11:63867772..63869724,2	K562	blood:
2	chr11:63867468..63869509-chr11:63890366..63892303,2	MCF-7	breast:

Variant related genes	Relation type
FLRT1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs592271	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs594461	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616563	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs635139	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638227	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651855	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666497	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672104	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs687581	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
5	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
6	nsv897653	chr11:63761169-63875456	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv897654	chr11:63772000-63875456	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
10	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
13	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
14	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
15	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
16	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs641378	TRPT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63853000-63871200	Enhancers	Brain Cingulate Gyrus	brain
2	chr11:63853000-63871600	Enhancers	Brain Substantia Nigra	brain
3	chr11:63853400-63871200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr11:63853600-63870800	Enhancers	Brain Angular Gyrus	brain
5	chr11:63856400-63871400	Enhancers	Brain Anterior Caudate	brain
6	chr11:63863600-63873200	Weak transcription	Colonic Mucosa	Colon
7	chr11:63863800-63875000	Weak transcription	Spleen	Spleen
8	chr11:63863800-63876600	Weak transcription	Fetal Intestine Small	intestine
9	chr11:63864800-63870000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:63865600-63872200	Weak transcription	Right Ventricle	heart
11	chr11:63866000-63878800	Weak transcription	Esophagus	oesophagus
12	chr11:63866400-63887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:63866800-63869800	Enhancers	Fetal Stomach	stomach
14	chr11:63867000-63882800	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:63867200-63872600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:63867400-63878400	Weak transcription	HepG2	liver
17	chr11:63867600-63872000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:63867800-63870200	Enhancers	Fetal Brain Male	brain
19	chr11:63867800-63871200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:63868000-63870200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr11:63868000-63870200	Enhancers	Psoas Muscle	Psoas
22	chr11:63868000-63871400	Enhancers	Brain Germinal Matrix	brain
23	chr11:63868000-63874400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr11:63868200-63870000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:63868200-63870000	Enhancers	Fetal Brain Female	brain
26	chr11:63868400-63870400	Enhancers	Ovary	ovary
27	chr11:63868400-63871000	Enhancers	Adipose Nuclei	Adipose
28	chr11:63868400-63873400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:63868600-63869800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:63868600-63869800	Enhancers	Rectal Smooth Muscle	rectum
31	chr11:63868600-63870000	Enhancers	HSMM	muscle
32	chr11:63868600-63871400	Enhancers	Fetal Thymus	thymus
33	chr11:63868800-63869600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
34	chr11:63869000-63870000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:63869200-63869600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:63869200-63869600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:63869200-63869600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:63869200-63869600	Enhancers	Fetal Intestine Large	intestine
39	chr11:63869200-63869600	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr11:63869200-63869600	Flanking Active TSS	NHDF-Ad	bronchial
41	chr11:63869200-63869800	Weak transcription	Fetal Lung	lung
42	chr11:63869200-63870000	Enhancers	Stomach Smooth Muscle	stomach
43	chr11:63869200-63870200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr11:63869200-63871600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:63869400-63869600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr11:63869400-63869800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr11:63869400-63871400	Enhancers	Brain Hippocampus Middle	brain

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