Variant report

Variant	rs1060639
Chromosome Location	chr12:124109988-124109989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124107277..124111165-chr12:124113286..124117641,5	MCF-7	breast:
2	chr12:124109158..124110697-chr12:124113991..124116759,2	K562	blood:
3	chr12:124105003..124107818-chr12:124109888..124111982,3	MCF-7	breast:
4	chr12:124107998..124110847-chr12:124196796..124199749,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185344	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1051793	0.84[EUR][1000 genomes]
rs1060637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846537	0.84[EUR][1000 genomes]
rs1139320	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11572920	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11572952	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11610473	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11611354	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611450	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11612030	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11612479	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11612927	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11613632	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11614155	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11614468	0.83[ASN][1000 genomes]
rs11614659	0.80[EUR][1000 genomes]
rs11615162	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11615300	0.88[EUR][1000 genomes]
rs11830462	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11831536	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11833604	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11834141	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11834492	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11834808	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12811354	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12813758	0.81[EUR][1000 genomes]
rs12817576	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12817757	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12818596	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12820195	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12821242	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12822546	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12823866	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12824075	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12827074	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12828408	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12829893	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12829984	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12830927	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12831081	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1515815	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962020	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2203500	0.83[ASN][1000 genomes]
rs2222060	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34534928	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35416308	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35649708	0.81[EUR][1000 genomes]
rs35804181	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35900897	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35946281	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36018806	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817309	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930708	0.84[EUR][1000 genomes]
rs4930737	0.81[AFR][1000 genomes]
rs6488888	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6488891	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6488892	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6488893	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6488894	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66471742	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66690784	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67178535	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7133543	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7133734	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7135267	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7135660	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136939	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71458814	0.81[EUR][1000 genomes]
rs7294984	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7296804	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7298440	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302649	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302788	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7304052	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7304837	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7305838	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7307008	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7307343	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7308234	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7309528	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7310918	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73219037	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7397160	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7397230	0.83[ASN][1000 genomes]
rs7397930	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7398152	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7398298	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7399224	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7953596	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7953599	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7957429	0.83[ASN][1000 genomes]
rs7959553	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7963498	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7963968	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7968029	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969130	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969234	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7969964	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7973155	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7973695	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7975119	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7975233	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7978447	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979528	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	nsv1040356	chr12:124094758-124172731	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1060639	TCTN2	cis	Skin Sun Exposed Lower leg	GTEx
rs1060639	TCTN2	cis	Muscle Skeletal	GTEx
rs1060639	ATP6V0A2	cis	Nerve Tibial	GTEx
rs1060639	TCTN2	cis	lung	GTEx
rs1060639	TCTN2	cis	Esophagus Muscularis	GTEx
rs1060639	TCTN2	cis	Artery Tibial	GTEx
rs1060639	TCTN2	cis	Nerve Tibial	GTEx
rs1060639	TCTN2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124088200-124116000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:124088200-124117000	Strong transcription	Fetal Stomach	stomach
3	chr12:124088400-124116000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:124088400-124116000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:124088400-124116000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:124088400-124116000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:124088400-124116000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:124088400-124116200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:124088400-124116800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:124088400-124117000	Strong transcription	Fetal Intestine Small	intestine
11	chr12:124088600-124116000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:124088600-124116000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:124088600-124116000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:124088600-124116000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:124088600-124116000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:124088600-124116000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:124088600-124116200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:124088600-124116200	Strong transcription	Fetal Thymus	thymus
19	chr12:124088600-124116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:124088600-124116800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:124088600-124116800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:124088600-124117000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:124088800-124116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:124088800-124116000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:124088800-124116000	Strong transcription	Fetal Intestine Large	intestine
26	chr12:124089000-124116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:124089000-124116200	Strong transcription	Brain Germinal Matrix	brain
28	chr12:124089200-124115400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:124089200-124116000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:124089200-124116000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:124089200-124116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:124089200-124116200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:124089200-124116400	Strong transcription	Liver	Liver
34	chr12:124089200-124116600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr12:124089600-124116000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:124089600-124116000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:124089600-124116000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr12:124089800-124116200	Strong transcription	Thymus	Thymus
39	chr12:124089800-124117000	Strong transcription	Placenta	Placenta
40	chr12:124090000-124115600	Strong transcription	GM12878-XiMat	blood
41	chr12:124090000-124116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:124090000-124116000	Strong transcription	Primary B cells from cord blood	blood
43	chr12:124090000-124116000	Strong transcription	Primary T cells from cord blood	blood
44	chr12:124090200-124116000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:124090200-124116000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:124090200-124116000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr12:124090200-124116200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:124090200-124116200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:124090200-124116200	Strong transcription	Brain Anterior Caudate	brain
50	chr12:124090200-124116800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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