Variant report

Variant	rs10734903
Chromosome Location	chr12:124202242-124202243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124201404..124203002-chr12:124209235..124211482,2	K562	blood:
2	chr12:124194853..124196399-chr12:124201524..124203920,2	K562	blood:
3	chr12:124201954..124203947-chr12:124204566..124207259,2	MCF-7	breast:
4	chr12:124197317..124199862-chr12:124200055..124203034,3	K562	blood:
5	chr12:124192727..124194757-chr12:124200394..124202441,2	K562	blood:

Variant related genes	Relation type
ENSG00000239215	Chromatin interaction
ENSG00000255839	Chromatin interaction

Extended variants
information (count: 170 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10160842	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10160937	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040156	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732574	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734904	0.89[EUR][1000 genomes]
rs10734905	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734906	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734907	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10734908	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744157	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744158	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744159	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744160	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744161	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744162	0.89[EUR][1000 genomes]
rs10773026	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773030	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773031	0.81[EUR][1000 genomes]
rs10773032	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773033	0.84[EUR][1000 genomes]
rs10773034	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846549	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10846550	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846551	0.81[EUR][1000 genomes]
rs10846553	0.94[EUR][1000 genomes]
rs1139320	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1139789	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	0.80[EUR][1000 genomes];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	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11837144	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580486	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811354	0.83[ASN][1000 genomes]
rs12813758	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12817576	0.86[ASN][1000 genomes]
rs12817757	0.83[ASN][1000 genomes]
rs12818596	0.80[EUR][1000 genomes];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	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12828408	0.81[EUR][1000 genomes];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	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878077	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176152	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2203500	0.83[ASN][1000 genomes]
rs2222060	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271660	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271661	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271662	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333834	0.89[EUR][1000 genomes]
rs2333835	0.87[EUR][1000 genomes]
rs2333836	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333837	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333838	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333839	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2333840	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34247974	0.90[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	0.81[EUR][1000 genomes];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	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488900	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488902	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66471742	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66647364	0.81[ASN][1000 genomes]
rs66690784	0.83[ASN][1000 genomes]
rs67178535	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7132115	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133543	0.83[ASN][1000 genomes]
rs7133734	0.87[ASN][1000 genomes]
rs7135267	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7135542	0.86[AMR][1000 genomes];0.99[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	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296804	0.83[ASN][1000 genomes]
rs7298440	0.83[ASN][1000 genomes]
rs7300721	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300818	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301641	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302649	0.83[ASN][1000 genomes]
rs7302708	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7307008	0.83[ASN][1000 genomes]
rs7307343	0.83[ASN][1000 genomes]
rs7308234	0.83[ASN][1000 genomes]
rs7308398	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309528	0.83[ASN][1000 genomes]
rs7310918	0.83[ASN][1000 genomes]
rs7311789	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219037	0.83[ASN][1000 genomes]
rs7397160	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7397230	0.83[ASN][1000 genomes]
rs7397240	0.81[EUR][1000 genomes]
rs7397745	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7397746	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7397930	0.83[ASN][1000 genomes]
rs7398082	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398152	0.83[ASN][1000 genomes]
rs7398298	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7398384	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7398606	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398641	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398851	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7399128	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7399224	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7953596	0.83[ASN][1000 genomes]
rs7953599	0.83[ASN][1000 genomes]
rs7956045	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956751	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7973695	0.83[ASN][1000 genomes]
rs7974331	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974462	0.85[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	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs968203	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787987	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788204	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
rs10734903	TCTN2	cis	Stomach	GTEx
rs10734903	TCTN2	cis	Artery Tibial	GTEx
rs10734903	TCTN2	cis	Thyroid	GTEx
rs10734903	TCTN2	cis	Esophagus Muscularis	GTEx
rs10734903	TCTN2	cis	lung	GTEx
rs10734903	TCTN2	cis	Adipose Subcutaneous	GTEx
rs10734903	TCTN2	cis	Nerve Tibial	GTEx
rs10734903	ATP6V0A2	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 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	chr12:124197800-124202600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:124198200-124203800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:124198200-124204400	Weak transcription	Aorta	Aorta
5	chr12:124198200-124207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:124198200-124207200	Weak transcription	Ovary	ovary
7	chr12:124198400-124203600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:124198400-124203800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:124198400-124203800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:124198400-124204400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:124198400-124204400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124198400-124210600	Weak transcription	NH-A	brain
13	chr12:124198600-124203400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:124198600-124203800	Weak transcription	HUVEC	blood vessel
15	chr12:124198600-124204000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:124198600-124204000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:124198600-124205000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:124198600-124205600	Weak transcription	HSMM	muscle
19	chr12:124198600-124205800	Weak transcription	HMEC	breast
20	chr12:124198600-124206800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:124198600-124207200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:124198600-124212400	Weak transcription	NHLF	lung
23	chr12:124198800-124202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:124198800-124203400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:124198800-124203600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:124198800-124203600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:124198800-124203800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:124198800-124204200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:124198800-124204200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:124198800-124204200	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:124198800-124204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:124198800-124204400	Weak transcription	Placenta	Placenta
33	chr12:124198800-124205000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:124198800-124205800	Weak transcription	A549	lung
35	chr12:124198800-124205800	Weak transcription	Osteobl	bone
36	chr12:124198800-124210800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:124198800-124223600	Weak transcription	Right Atrium	heart
38	chr12:124199000-124203600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:124199000-124203600	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:124199000-124203800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:124199000-124203800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:124199000-124203800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:124199000-124203800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:124199000-124204000	Weak transcription	Right Ventricle	heart
45	chr12:124199000-124204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:124199000-124204200	Weak transcription	Left Ventricle	heart
47	chr12:124199000-124204200	Weak transcription	Lung	lung
48	chr12:124199000-124204200	Weak transcription	HSMMtube	muscle
49	chr12:124199000-124204400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:124199000-124204400	Weak transcription	Brain Inferior Temporal Lobe	brain

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