Variant report

Variant	rs12821219
Chromosome Location	chr12:124178290-124178291
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124176790..124178829-chr12:124179921..124182332,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10846535	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10846540	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846541	0.92[ASN][1000 genomes]
rs10846546	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057307	0.81[EUR][1000 genomes]
rs11057320	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11609591	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11614659	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11829958	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12813346	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12819746	0.82[EUR][1000 genomes]
rs12825800	0.82[EUR][1000 genomes]
rs12828633	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1515814	0.82[EUR][1000 genomes]
rs1969272	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2222061	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250026	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35114195	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35158437	0.83[EUR][1000 genomes]
rs3748269	0.81[EUR][1000 genomes]
rs6488883	0.81[EUR][1000 genomes]
rs6488897	0.82[EUR][1000 genomes]
rs66647364	0.81[EUR][1000 genomes]
rs7134074	0.83[EUR][1000 genomes]
rs7134896	0.81[EUR][1000 genomes]
rs7135624	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7137946	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138503	0.82[EUR][1000 genomes]
rs7139193	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297576	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7298831	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7301907	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302183	0.81[EUR][1000 genomes]
rs7302449	0.97[AFR][1000 genomes];0.99[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	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7313032	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7313140	0.83[EUR][1000 genomes]
rs7313261	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7313628	0.82[EUR][1000 genomes]
rs7958693	0.83[EUR][1000 genomes]
rs7960951	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7964443	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7966867	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966882	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7971452	0.86[AMR][1000 genomes]
rs7974279	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1041918	chr12:124115035-124184855	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	nsv524660	chr12:124119983-124194438	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	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
13	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
14	nsv1044734	chr12:124127003-124179417	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	nsv519344	chr12:124171903-124194438	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12821219	TCTN2	cis	Artery Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124156200-124182000	Weak transcription	Small Intestine	intestine
2	chr12:124156400-124196000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:124156400-124196000	Weak transcription	Thymus	Thymus
4	chr12:124156600-124180600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:124156600-124189800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:124156600-124195600	Weak transcription	Esophagus	oesophagus
7	chr12:124156600-124195800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:124156600-124195800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:124156600-124196000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:124156600-124196000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:124156600-124196000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:124156600-124196000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:124156800-124180200	Weak transcription	Stomach Mucosa	stomach
14	chr12:124156800-124181000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:124156800-124181000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:124156800-124184000	Weak transcription	HepG2	liver
17	chr12:124156800-124186600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:124156800-124196000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:124156800-124196000	Weak transcription	HUVEC	blood vessel
20	chr12:124156800-124196200	Weak transcription	HSMM	muscle
21	chr12:124157000-124193000	Strong transcription	Fetal Stomach	stomach
22	chr12:124157000-124196000	Weak transcription	Fetal Heart	heart
23	chr12:124157000-124196000	Weak transcription	NH-A	brain
24	chr12:124158400-124193800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:124159800-124183800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:124160000-124181400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:124160000-124184400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:124160000-124195600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:124160200-124180600	Weak transcription	Fetal Kidney	kidney
30	chr12:124160200-124191000	Weak transcription	Colonic Mucosa	Colon
31	chr12:124160200-124195800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:124160200-124196000	Weak transcription	Right Ventricle	heart
33	chr12:124160400-124181000	Weak transcription	NHDF-Ad	bronchial
34	chr12:124160800-124181000	Weak transcription	Primary T cells from cord blood	blood
35	chr12:124160800-124182800	Weak transcription	Dnd41	blood
36	chr12:124161600-124196000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:124161800-124180800	Weak transcription	Fetal Brain Male	brain
38	chr12:124161800-124183000	Weak transcription	Placenta	Placenta
39	chr12:124161800-124195800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:124164000-124179000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:124164200-124186600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:124164200-124195800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:124164200-124196000	Weak transcription	Fetal Thymus	thymus
44	chr12:124166200-124195800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:124166800-124178400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:124166800-124178600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:124166800-124183200	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:124166800-124189000	Weak transcription	HSMMtube	muscle
49	chr12:124166800-124196000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:124168400-124184800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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