Variant report

Variant	rs10744159
Chromosome Location	chr12:124218359-124218360
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124208285..124210761-chr12:124216030..124218453,2	MCF-7	breast:
2	chr12:124116224..124118107-chr12:124217951..124220255,2	MCF-7	breast:
3	chr12:124205928..124208460-chr12:124216017..124218641,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239215	Chromatin interaction
ENSG00000185344	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10160842	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10160937	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040156	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732574	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734903	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734904	0.91[EUR][1000 genomes]
rs10734905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734907	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10734908	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744157	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744158	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744160	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744161	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744162	0.86[EUR][1000 genomes]
rs10773026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773031	0.83[EUR][1000 genomes]
rs10773032	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773033	0.81[EUR][1000 genomes]
rs10773034	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846549	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10846550	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846551	0.83[EUR][1000 genomes]
rs10846553	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1139320	0.87[ASN][1000 genomes]
rs1139789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572920	0.86[ASN][1000 genomes]
rs11572952	0.86[ASN][1000 genomes]
rs11611354	0.83[ASN][1000 genomes]
rs11611450	0.83[ASN][1000 genomes]
rs11612030	0.83[ASN][1000 genomes]
rs11612479	0.83[ASN][1000 genomes]
rs11612927	0.86[ASN][1000 genomes]
rs11613632	0.83[ASN][1000 genomes]
rs11614155	0.83[ASN][1000 genomes]
rs11614468	0.83[ASN][1000 genomes]
rs11615162	0.86[ASN][1000 genomes]
rs11830462	0.83[ASN][1000 genomes]
rs11831536	0.83[ASN][1000 genomes]
rs11833604	0.83[ASN][1000 genomes]
rs11834492	0.83[ASN][1000 genomes]
rs11834808	0.83[ASN][1000 genomes]
rs11837144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580486	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811354	0.83[ASN][1000 genomes]
rs12813758	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12817576	0.86[ASN][1000 genomes]
rs12817757	0.83[ASN][1000 genomes]
rs12818596	0.83[ASN][1000 genomes]
rs12820195	0.83[ASN][1000 genomes]
rs12821242	0.83[ASN][1000 genomes]
rs12822546	0.83[ASN][1000 genomes]
rs12823866	0.83[ASN][1000 genomes]
rs12824075	0.83[ASN][1000 genomes]
rs12827074	0.83[ASN][1000 genomes]
rs12828408	0.87[ASN][1000 genomes]
rs12829893	0.83[ASN][1000 genomes]
rs12829984	0.83[ASN][1000 genomes]
rs12830927	0.86[ASN][1000 genomes]
rs12831081	0.83[ASN][1000 genomes]
rs1399961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878077	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176152	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2203500	0.83[ASN][1000 genomes]
rs2222060	0.83[ASN][1000 genomes]
rs2271660	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271661	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333834	0.86[EUR][1000 genomes]
rs2333835	0.89[EUR][1000 genomes]
rs2333836	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333837	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333838	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333839	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34247974	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34534928	0.83[ASN][1000 genomes]
rs34996665	0.83[ASN][1000 genomes]
rs35416308	0.83[ASN][1000 genomes]
rs35804181	0.83[ASN][1000 genomes]
rs35900897	0.80[ASN][1000 genomes]
rs35911711	0.81[ASN][1000 genomes]
rs35946281	0.83[ASN][1000 genomes]
rs3817309	0.87[ASN][1000 genomes]
rs6488888	0.80[ASN][1000 genomes]
rs6488891	0.83[ASN][1000 genomes]
rs6488892	0.83[ASN][1000 genomes]
rs6488893	0.83[ASN][1000 genomes]
rs6488894	0.83[ASN][1000 genomes]
rs6488899	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488900	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488902	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66471742	0.87[ASN][1000 genomes]
rs66647364	0.81[ASN][1000 genomes]
rs66690784	0.83[ASN][1000 genomes]
rs67178535	0.83[ASN][1000 genomes]
rs7132115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133543	0.83[ASN][1000 genomes]
rs7133734	0.87[ASN][1000 genomes]
rs7135267	0.87[ASN][1000 genomes]
rs7135542	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135660	0.83[ASN][1000 genomes]
rs7136939	0.83[ASN][1000 genomes]
rs7294984	0.80[ASN][1000 genomes]
rs7295552	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296804	0.83[ASN][1000 genomes]
rs7298440	0.83[ASN][1000 genomes]
rs7300721	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7301641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302649	0.83[ASN][1000 genomes]
rs7302708	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7302788	0.83[ASN][1000 genomes]
rs7304052	0.83[ASN][1000 genomes]
rs7304837	0.83[ASN][1000 genomes]
rs7305838	0.83[ASN][1000 genomes]
rs7307008	0.83[ASN][1000 genomes]
rs7307343	0.83[ASN][1000 genomes]
rs7308234	0.83[ASN][1000 genomes]
rs7308398	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309528	0.83[ASN][1000 genomes]
rs7310918	0.83[ASN][1000 genomes]
rs7311789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219037	0.83[ASN][1000 genomes]
rs7397160	0.83[ASN][1000 genomes]
rs7397230	0.83[ASN][1000 genomes]
rs7397240	0.84[EUR][1000 genomes]
rs7397745	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7397746	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7397930	0.83[ASN][1000 genomes]
rs7398082	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398152	0.83[ASN][1000 genomes]
rs7398298	0.83[ASN][1000 genomes]
rs7398384	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7398606	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398641	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398851	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7399128	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7399224	0.83[ASN][1000 genomes]
rs7953596	0.83[ASN][1000 genomes]
rs7953599	0.83[ASN][1000 genomes]
rs7956045	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956751	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957429	0.83[ASN][1000 genomes]
rs7959553	0.83[ASN][1000 genomes]
rs7960017	0.82[ASN][1000 genomes]
rs7960403	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963498	0.83[ASN][1000 genomes]
rs7963968	0.83[ASN][1000 genomes]
rs7968029	0.83[ASN][1000 genomes]
rs7969130	0.83[ASN][1000 genomes]
rs7969234	0.83[ASN][1000 genomes]
rs7969964	0.83[ASN][1000 genomes]
rs7973155	0.83[ASN][1000 genomes]
rs7973695	0.83[ASN][1000 genomes]
rs7974331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974462	0.87[EUR][1000 genomes]
rs7975119	0.83[ASN][1000 genomes]
rs7975233	0.83[ASN][1000 genomes]
rs7978447	0.83[ASN][1000 genomes]
rs7979528	0.83[ASN][1000 genomes]
rs882563	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs968203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788204	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10744159	TCTN2	cis	lung	GTEx
rs10744159	TCTN2	cis	Stomach	GTEx
rs10744159	TCTN2	cis	Esophagus Muscularis	GTEx
rs10744159	TCTN2	cis	Adipose Subcutaneous	GTEx
rs10744159	TCTN2	cis	Thyroid	GTEx
rs10744159	ATP6V0A2	cis	Nerve Tibial	GTEx
rs10744159	TCTN2	cis	Artery Tibial	GTEx
rs10744159	TCTN2	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124197600-124234400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:124198800-124223600	Weak transcription	Right Atrium	heart
3	chr12:124199600-124221000	Weak transcription	Psoas Muscle	Psoas
4	chr12:124201800-124247800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:124202200-124242600	Strong transcription	Fetal Stomach	stomach
6	chr12:124202600-124245200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:124202600-124245200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:124203000-124230600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:124203400-124239800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:124203600-124221000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:124203600-124242400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:124203600-124242400	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:124203600-124244600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:124203600-124246000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:124203800-124240000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:124203800-124245000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:124203800-124248000	Strong transcription	Dnd41	blood
18	chr12:124204000-124222400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:124204000-124235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:124204000-124235800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:124204000-124239800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:124204200-124230000	Strong transcription	Fetal Brain Female	brain
23	chr12:124204400-124230000	Strong transcription	Placenta	Placenta
24	chr12:124205000-124242400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:124205400-124233200	Weak transcription	Stomach Mucosa	stomach
26	chr12:124206000-124241800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:124206200-124237200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:124206400-124237600	Strong transcription	Adipose Nuclei	Adipose
29	chr12:124208000-124221400	Weak transcription	Small Intestine	intestine
30	chr12:124208600-124218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:124208600-124221200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:124208600-124221400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:124208800-124221400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr12:124208800-124226200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:124208800-124244800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:124209000-124221400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:124209000-124226600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:124209200-124222200	Strong transcription	Left Ventricle	heart
39	chr12:124209200-124226600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:124209200-124226600	Strong transcription	Fetal Thymus	thymus
41	chr12:124209200-124236000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:124209200-124242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:124209400-124221200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:124209400-124226600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:124209600-124224400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:124209800-124239600	Strong transcription	Brain Germinal Matrix	brain
47	chr12:124210000-124224400	Strong transcription	Colon Smooth Muscle	Colon
48	chr12:124210000-124230800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:124210600-124218800	Strong transcription	Primary B cells from cord blood	blood
50	chr12:124210600-124224400	Strong transcription	HSMM	muscle

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