Variant report

Variant	rs10846553
Chromosome Location	chr12:124244272-124244273
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	POLR2A	chr12:124244009-124245369	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124243395..124246138-chr12:124246232..124249916,3	K562	blood:

Variant related genes	Relation type
DNAH10	TF binding region
ENSG00000197653	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10160842	0.90[EUR][1000 genomes]
rs10160937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs1040156	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1051793	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1060637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732574	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10734903	0.94[EUR][1000 genomes]
rs10734904	0.84[EUR][1000 genomes]
rs10734905	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10734906	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10734907	0.84[EUR][1000 genomes]
rs10734908	0.85[EUR][1000 genomes]
rs10744157	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744159	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10744161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10744162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773026	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10773030	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10773032	0.85[EUR][1000 genomes]
rs10773034	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10846537	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10846549	0.85[EUR][1000 genomes]
rs10846550	0.85[EUR][1000 genomes]
rs1139789	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11572920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11572952	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11609591	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611354	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612030	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612479	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612927	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11613632	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11837144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12580486	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12817757	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12820195	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12821242	0.83[CEU][hapmap]
rs12827074	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12829893	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12830927	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1399961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1515815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1878077	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2176152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2222060	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2271660	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2271661	0.85[EUR][1000 genomes]
rs2271662	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2333834	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2333835	0.82[EUR][1000 genomes]
rs2333836	0.85[EUR][1000 genomes]
rs2333837	0.83[EUR][1000 genomes]
rs2333838	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2333839	0.85[EUR][1000 genomes]
rs2333840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34247974	0.85[EUR][1000 genomes]
rs4930708	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488888	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6488893	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488897	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488899	0.91[EUR][1000 genomes]
rs6488900	0.90[EUR][1000 genomes]
rs6488902	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7132115	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7133199	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134074	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7135542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7135660	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136939	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7294984	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7295552	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7297576	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298440	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298831	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7300721	0.85[EUR][1000 genomes]
rs7300818	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7301641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7302649	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7302708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7306549	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7307008	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7307343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7308234	0.82[CEU][hapmap]
rs7308398	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7308862	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7309528	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7310918	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7311789	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7313032	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7313261	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7397745	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7397746	0.85[EUR][1000 genomes]
rs7398082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7398384	0.84[EUR][1000 genomes]
rs7398606	0.91[EUR][1000 genomes]
rs7398641	0.85[EUR][1000 genomes]
rs7398851	0.85[EUR][1000 genomes]
rs7399128	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7399224	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7953599	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7956045	0.90[EUR][1000 genomes]
rs7956751	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7958693	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7959553	0.84[CEU][hapmap]
rs7960403	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7963968	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7964443	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7973155	0.84[CEU][hapmap]
rs7973695	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7974279	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7974331	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7975119	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7975233	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7978447	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7979528	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs882563	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs968203	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9787987	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9788204	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10846553	ATP6V0A2	cis	Nerve Tibial	GTEx
rs10846553	TCTN2	cis	lung	GTEx
rs10846553	TCTN2	cis	Adipose Subcutaneous	GTEx
rs10846553	TCTN2	cis	Artery Tibial	GTEx
rs10846553	TCTN2	cis	Nerve Tibial	GTEx
rs10846553	TCTN2	cis	Thyroid	GTEx
rs10846553	TCTN2	cis	Stomach	GTEx
rs10846553	TCTN2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124201800-124247800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:124202600-124245200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:124202600-124245200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:124203600-124244600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:124203600-124246000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:124203800-124245000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:124203800-124248000	Strong transcription	Dnd41	blood
8	chr12:124208800-124244800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:124215400-124244800	Strong transcription	Liver	Liver
10	chr12:124221800-124246200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:124224200-124246400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:124229800-124246400	Weak transcription	Psoas Muscle	Psoas
13	chr12:124230200-124246000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:124232000-124246400	Weak transcription	NHDF-Ad	bronchial
15	chr12:124233600-124245000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:124233600-124245400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:124233800-124245400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:124234200-124247400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:124234400-124245000	Weak transcription	HepG2	liver
20	chr12:124234400-124246000	Weak transcription	Hela-S3	cervix
21	chr12:124234800-124246400	Weak transcription	Stomach Mucosa	stomach
22	chr12:124235000-124246200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:124235400-124246000	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:124235400-124246400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:124235800-124244400	Weak transcription	Fetal Brain Male	brain
26	chr12:124237200-124245400	Strong transcription	Primary hematopoietic stem cells	blood
27	chr12:124239600-124245800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:124239600-124246000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:124239600-124246000	Weak transcription	Placenta	Placenta
30	chr12:124239600-124246000	Weak transcription	NHEK	skin
31	chr12:124239600-124246200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:124239600-124246200	Weak transcription	NH-A	brain
33	chr12:124239800-124245800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:124239800-124245800	Weak transcription	Fetal Heart	heart
35	chr12:124239800-124246000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:124239800-124246000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:124239800-124246000	Weak transcription	Fetal Kidney	kidney
38	chr12:124239800-124246000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:124239800-124246000	Weak transcription	HUVEC	blood vessel
40	chr12:124239800-124246200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:124239800-124246200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:124239800-124246200	Weak transcription	Brain Anterior Caudate	brain
43	chr12:124239800-124246200	Weak transcription	Colonic Mucosa	Colon
44	chr12:124239800-124246400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:124239800-124246400	Weak transcription	Aorta	Aorta
46	chr12:124239800-124246400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:124239800-124246400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:124239800-124246400	Weak transcription	HMEC	breast
49	chr12:124239800-124246800	Weak transcription	Brain Angular Gyrus	brain
50	chr12:124239800-124247200	Weak transcription	HSMM	muscle

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