Variant report

Variant	rs6551
Chromosome Location	chr12:124082240-124082241
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124081632-124084546	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:124080492-124084849	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:124065661..124069328-chr12:124081746..124084446,4	K562	blood:
2	chr12:123848402..123850885-chr12:124079862..124083002,3	MCF-7	breast:
3	chr12:124080644..124082674-chr12:124097166..124099326,2	K562	blood:
4	chr12:123755326..123757299-chr12:124079928..124082713,2	MCF-7	breast:
5	chr12:124081195..124083992-chr12:124117533..124119708,3	MCF-7	breast:
6	chr12:124075051..124078239-chr12:124079848..124084285,5	K562	blood:
7	chr12:123752131..123754716-chr12:124081309..124084264,2	MCF-7	breast:
8	chr12:124069965..124078255-chr12:124078837..124084347,12	K562	blood:

No data

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111364	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10846531	0.84[ASN][1000 genomes]
rs10846535	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057307	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.80[EUR][1000 genomes]
rs11615300	0.81[EUR][1000 genomes]
rs1515814	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048802	0.84[ASN][1000 genomes]
rs3748268	0.84[ASN][1000 genomes]
rs3748269	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488883	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302183	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313628	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.90[ASN][1000 genomes]
rs7966882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7972413	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884892	0.84[ASN][1000 genomes]
rs908373	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6551	TCTN2	cis	Adipose Subcutaneous	GTEx
rs6551	TCTN2	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:124071200-124082800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:124071200-124083400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:124071200-124083400	Strong transcription	Fetal Intestine Large	intestine
6	chr12:124071200-124083600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:124071200-124083600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:124071200-124083600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr12:124071200-124083800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:124071200-124083800	Strong transcription	Placenta	Placenta
11	chr12:124071200-124084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:124071200-124084000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:124071200-124084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:124071400-124082800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr12:124071400-124083000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:124071600-124084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:124071800-124083600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
19	chr12:124072400-124083800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:124072600-124082400	Strong transcription	Thymus	Thymus
21	chr12:124072600-124083400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:124072600-124083400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:124072800-124084200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:124073000-124083600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:124073200-124084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:124073400-124082400	Strong transcription	NHEK	skin
27	chr12:124073400-124084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:124073600-124082400	Strong transcription	Fetal Brain Female	brain
29	chr12:124073600-124083400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:124073600-124083600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:124073600-124083800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:124073600-124083800	Strong transcription	Left Ventricle	heart
33	chr12:124073800-124083000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr12:124073800-124083200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:124073800-124083400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr12:124073800-124083600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr12:124073800-124083800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:124073800-124083800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr12:124073800-124084200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:124073800-124084600	Strong transcription	Fetal Thymus	thymus
41	chr12:124073800-124085200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:124073800-124085400	Weak transcription	Stomach Mucosa	stomach
43	chr12:124074000-124083200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:124074000-124083800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:124074000-124084400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:124074200-124082600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:124074200-124086000	Weak transcription	Fetal Heart	heart
48	chr12:124075000-124084000	Strong transcription	Brain Substantia Nigra	brain
49	chr12:124075000-124084200	Strong transcription	Dnd41	blood
50	chr12:124075200-124085600	Weak transcription	Right Ventricle	heart

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