Variant report

Variant	rs6488902
Chromosome Location	chr12:124205046-124205047
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:124203615-124205390	K562	blood:	n/a	n/a
2	ATF1	chr12:124204167-124205067	K562	blood:	n/a	n/a
3	MAX	chr12:124204927-124205283	K562	blood:	n/a	n/a
4	IRF1	chr12:124203593-124205073	K562	blood:	n/a	n/a
5	JUND	chr12:124203734-124205205	K562	blood:	n/a	chr12:124204845-124204852 chr12:124204843-124204852 chr12:124204842-124204854

Variant related genes	Relation type
ATP6V0A2	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10160842	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10160937	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1040156	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10732574	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734903	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734904	0.90[EUR][1000 genomes]
rs10734905	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734906	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734907	0.89[EUR][1000 genomes]
rs10734908	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10744157	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744158	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744159	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744160	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10744161	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744162	0.85[EUR][1000 genomes]
rs10773026	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773030	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773031	0.84[EUR][1000 genomes]
rs10773032	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773033	0.80[EUR][1000 genomes]
rs10773034	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10846549	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846550	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846551	0.84[EUR][1000 genomes]
rs10846553	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1139789	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11837144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580486	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813758	0.80[EUR][1000 genomes]
rs1399961	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1878077	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2176152	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271660	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271661	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271662	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333834	0.85[EUR][1000 genomes]
rs2333835	0.88[EUR][1000 genomes]
rs2333836	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333837	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2333838	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333839	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2333840	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34247974	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6488899	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6488900	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132115	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7135542	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7295552	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7300721	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7300818	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7301641	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7302708	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308398	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311789	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7397240	0.85[EUR][1000 genomes]
rs7397745	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7397746	0.91[EUR][1000 genomes]
rs7398082	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7398384	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7398606	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7398641	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7398851	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7399128	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956045	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7956751	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7960403	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974331	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974462	0.86[EUR][1000 genomes]
rs882563	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs968203	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787987	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788204	0.91[EUR][1000 genomes];0.84[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
rs6488902	ATP6V0A2	cis	Nerve Tibial	GTEx
rs6488902	TCTN2	cis	Nerve Tibial	GTEx
rs6488902	TCTN2	cis	Adipose Subcutaneous	GTEx
rs6488902	TCTN2	cis	Thyroid	GTEx
rs6488902	TCTN2	cis	Artery Tibial	GTEx
rs6488902	TCTN2	cis	Stomach	GTEx
rs6488902	TCTN2	cis	lung	GTEx
rs6488902	TCTN2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 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	chr12:124198200-124207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:124198200-124207200	Weak transcription	Ovary	ovary
4	chr12:124198400-124210600	Weak transcription	NH-A	brain
5	chr12:124198600-124205600	Weak transcription	HSMM	muscle
6	chr12:124198600-124205800	Weak transcription	HMEC	breast
7	chr12:124198600-124206800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:124198600-124207200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:124198600-124212400	Weak transcription	NHLF	lung
10	chr12:124198800-124205800	Weak transcription	A549	lung
11	chr12:124198800-124205800	Weak transcription	Osteobl	bone
12	chr12:124198800-124210800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:124198800-124223600	Weak transcription	Right Atrium	heart
14	chr12:124199000-124205600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:124199000-124206000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:124199000-124206000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:124199000-124206200	Weak transcription	NHEK	skin
18	chr12:124199000-124207000	Weak transcription	Fetal Kidney	kidney
19	chr12:124199000-124207200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:124199000-124207200	Weak transcription	Esophagus	oesophagus
21	chr12:124199000-124210000	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:124199000-124212400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:124199200-124205800	Weak transcription	Spleen	Spleen
24	chr12:124199200-124206000	Weak transcription	HepG2	liver
25	chr12:124199200-124206200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:124199200-124206400	Weak transcription	Adipose Nuclei	Adipose
27	chr12:124199200-124207200	Weak transcription	Small Intestine	intestine
28	chr12:124199200-124210000	Weak transcription	Colonic Mucosa	Colon
29	chr12:124199200-124210400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:124199200-124210600	Weak transcription	Hela-S3	cervix
31	chr12:124199200-124212400	Weak transcription	Fetal Lung	lung
32	chr12:124199200-124213200	Weak transcription	Pancreas	Pancrea
33	chr12:124199600-124207200	Weak transcription	Gastric	stomach
34	chr12:124199600-124221000	Weak transcription	Psoas Muscle	Psoas
35	chr12:124200000-124207000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:124200000-124207800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:124200200-124207200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:124200200-124208200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:124200200-124210600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:124200200-124210800	Weak transcription	NHDF-Ad	bronchial
41	chr12:124201200-124207400	Weak transcription	GM12878-XiMat	blood
42	chr12:124201400-124207000	Weak transcription	Fetal Brain Male	brain
43	chr12:124201800-124247800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:124202200-124242600	Strong transcription	Fetal Stomach	stomach
45	chr12:124202600-124207800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr12:124202600-124245200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:124202600-124245200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:124203000-124208200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:124203000-124230600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:124203400-124207800	Strong transcription	Rectal Mucosa Donor 31	rectum

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