Variant report

Variant	rs7960403
Chromosome Location	chr12:124209917-124209918
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124209327..124212221-chr12:124456476..124458926,2	K562	blood:
2	chr12:124201404..124203002-chr12:124209235..124211482,2	K562	blood:
3	chr12:124209785..124212605-chr12:124214306..124217027,2	MCF-7	breast:
4	chr12:124208285..124210761-chr12:124216030..124218453,2	MCF-7	breast:
5	chr12:124209327..124212228-chr12:124456476..124458926,3	K562	blood:
6	chr12:124209673..124212199-chr12:124234524..124236893,2	K562	blood:

Variant related genes	Relation type
ENSG00000179195	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000185344	Chromatin interaction
ENSG00000178882	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	0.98[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	0.85[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734906	0.96[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744159	0.96[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	0.96[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	0.96[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	0.96[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878077	0.95[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	0.96[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	0.96[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	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488902	0.96[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	0.96[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7301641	0.96[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	0.96[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	0.96[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	0.99[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	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956751	0.96[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]
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	0.96[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787987	0.96[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: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
rs7960403	TCTN2	cis	Thyroid	GTEx
rs7960403	TCTN2	cis	Stomach	GTEx
rs7960403	TCTN2	cis	Esophagus Muscularis	GTEx
rs7960403	TCTN2	cis	Artery Tibial	GTEx
rs7960403	TCTN2	cis	lung	GTEx
rs7960403	ATP6V0A2	cis	Nerve Tibial	GTEx
rs7960403	TCTN2	cis	Nerve Tibial	GTEx
rs7960403	TCTN2	cis	Adipose Subcutaneous	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	chr12:124198400-124210600	Weak transcription	NH-A	brain
3	chr12:124198600-124212400	Weak transcription	NHLF	lung
4	chr12:124198800-124210800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:124198800-124223600	Weak transcription	Right Atrium	heart
6	chr12:124199000-124210000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:124199000-124212400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:124199200-124210000	Weak transcription	Colonic Mucosa	Colon
9	chr12:124199200-124210400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:124199200-124210600	Weak transcription	Hela-S3	cervix
11	chr12:124199200-124212400	Weak transcription	Fetal Lung	lung
12	chr12:124199200-124213200	Weak transcription	Pancreas	Pancrea
13	chr12:124199600-124221000	Weak transcription	Psoas Muscle	Psoas
14	chr12:124200200-124210600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:124200200-124210800	Weak transcription	NHDF-Ad	bronchial
16	chr12:124201800-124247800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:124202200-124242600	Strong transcription	Fetal Stomach	stomach
18	chr12:124202600-124245200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:124202600-124245200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:124203000-124230600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:124203400-124214200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr12:124203400-124239800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:124203600-124221000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:124203600-124242400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:124203600-124242400	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:124203600-124244600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:124203600-124246000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:124203800-124214600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:124203800-124216000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:124203800-124240000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:124203800-124245000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:124203800-124248000	Strong transcription	Dnd41	blood
33	chr12:124204000-124222400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:124204000-124235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:124204000-124235800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr12:124204000-124239800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:124204200-124210000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:124204200-124214600	Strong transcription	Liver	Liver
39	chr12:124204200-124230000	Strong transcription	Fetal Brain Female	brain
40	chr12:124204400-124230000	Strong transcription	Placenta	Placenta
41	chr12:124204600-124212400	Weak transcription	Right Ventricle	heart
42	chr12:124204800-124211400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:124205000-124242400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:124205200-124212200	Weak transcription	Fetal Heart	heart
45	chr12:124205400-124210600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:124205400-124217000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:124205400-124233200	Weak transcription	Stomach Mucosa	stomach
48	chr12:124206000-124241800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:124206200-124237200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:124206400-124210000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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