Variant report

Variant	rs2222061
Chromosome Location	chr12:124194929-124194930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:124194853..124196399-chr12:124201524..124203920,2	K562	blood:
2	chr12:123716636..123719388-chr12:124194108..124196844,2	K562	blood:
3	chr12:124116424..124121252-chr12:124194298..124198817,7	K562	blood:
4	chr12:124190696..124192494-chr12:124194252..124196865,2	K562	blood:
5	chr12:123716636..123719469-chr12:124192807..124195608,2	K562	blood:
6	chr12:124185982..124187602-chr12:124193943..124196577,2	K562	blood:
7	chr12:124191295..124193347-chr12:124194777..124198625,4	MCF-7	breast:
8	chr12:124188235..124191139-chr12:124193941..124195953,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111361	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000255839	Chromatin interaction
ENSG00000111358	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10846535	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10846540	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846541	0.92[ASN][1000 genomes]
rs10846546	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057307	0.81[EUR][1000 genomes]
rs11057320	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11609591	0.83[EUR][1000 genomes]
rs11614659	0.82[EUR][1000 genomes]
rs11829958	0.83[EUR][1000 genomes]
rs12813346	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12819746	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12821219	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825800	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12828633	0.83[EUR][1000 genomes]
rs1515814	0.82[EUR][1000 genomes]
rs1969272	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2250026	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35114195	0.83[EUR][1000 genomes]
rs35158437	0.83[EUR][1000 genomes]
rs3748269	0.81[EUR][1000 genomes]
rs6488883	0.81[EUR][1000 genomes]
rs6488897	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66647364	0.83[EUR][1000 genomes]
rs7134074	0.83[EUR][1000 genomes]
rs7134896	0.81[EUR][1000 genomes]
rs7135624	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7137946	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138503	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7139193	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297576	0.83[EUR][1000 genomes]
rs7298831	0.83[EUR][1000 genomes]
rs7301907	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302183	0.81[EUR][1000 genomes]
rs7302449	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305701	0.82[EUR][1000 genomes]
rs7306549	0.83[EUR][1000 genomes]
rs7308862	0.83[EUR][1000 genomes]
rs7313032	0.83[EUR][1000 genomes]
rs7313140	0.83[EUR][1000 genomes]
rs7313261	0.83[EUR][1000 genomes]
rs7313628	0.82[EUR][1000 genomes]
rs7958693	0.83[EUR][1000 genomes]
rs7960951	0.82[EUR][1000 genomes]
rs7964443	0.82[EUR][1000 genomes]
rs7966867	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966882	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7971452	0.83[AMR][1000 genomes]
rs7974279	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv2757517	chr12:124110122-124195856	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv2759918	chr12:124110122-124195856	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
6	nsv1042866	chr12:124115035-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv442292	chr12:124115047-124195854	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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
8	esv35148	chr12:124119120-124196120	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv2756516	chr12:124119120-124196120	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv455733	chr12:124119983-124195856	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv560496	chr12:124119983-124195856	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv560497	chr12:124129460-124195856	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv560498	chr12:124129924-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv832534	chr12:124157605-124234611	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2222061	TCTN2	cis	Adipose Subcutaneous	GTEx
rs2222061	TCTN2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124156400-124196000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr12:124156400-124196000	Weak transcription	Thymus	Thymus
3	chr12:124156600-124195600	Weak transcription	Esophagus	oesophagus
4	chr12:124156600-124195800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:124156600-124195800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:124156600-124196000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:124156600-124196000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:124156600-124196000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:124156600-124196000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:124156800-124196000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:124156800-124196000	Weak transcription	HUVEC	blood vessel
12	chr12:124156800-124196200	Weak transcription	HSMM	muscle
13	chr12:124157000-124196000	Weak transcription	Fetal Heart	heart
14	chr12:124157000-124196000	Weak transcription	NH-A	brain
15	chr12:124160000-124195600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:124160200-124195800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:124160200-124196000	Weak transcription	Right Ventricle	heart
18	chr12:124161600-124196000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:124161800-124195800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:124164200-124195800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:124164200-124196000	Weak transcription	Fetal Thymus	thymus
22	chr12:124166200-124195800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:124166800-124196000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:124173400-124196000	Weak transcription	GM12878-XiMat	blood
25	chr12:124176000-124195800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:124176200-124195800	Weak transcription	HMEC	breast
27	chr12:124176200-124196200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:124176200-124196400	Weak transcription	Gastric	stomach
29	chr12:124177600-124195800	Weak transcription	Hela-S3	cervix
30	chr12:124181200-124195800	Weak transcription	Stomach Mucosa	stomach
31	chr12:124181600-124196000	Weak transcription	Primary T cells from cord blood	blood
32	chr12:124181800-124195800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:124182000-124196000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:124182400-124195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:124184800-124195800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr12:124184800-124196000	Weak transcription	Fetal Kidney	kidney
37	chr12:124185000-124195800	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:124185000-124195800	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:124185000-124195800	Weak transcription	Placenta	Placenta
40	chr12:124185000-124196000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:124185000-124196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:124185400-124195800	Weak transcription	Lung	lung
43	chr12:124185400-124195800	Weak transcription	HepG2	liver
44	chr12:124185400-124196000	Weak transcription	Left Ventricle	heart
45	chr12:124185600-124195800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:124185600-124196000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:124185800-124196000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:124185800-124196200	Weak transcription	NHLF	lung
49	chr12:124186000-124195800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:124186800-124196200	Weak transcription	Placenta Amnion	Placenta Amnion

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