Variant report

Variant	rs2333834
Chromosome Location	chr12:124246004-124246005
allele	C/T
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	chr12:124245802-124247997	K562	blood:	n/a	n/a
2	MXI1	chr12:124245970-124247083	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:124245875-124246160	H1-neurons	neurons:	n/a	n/a
4	MTA3	chr12:124245677-124247263	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124243395..124246138-chr12:124246232..124249916,3	K562	blood:
2	chr12:124238409..124242727-chr12:124245328..124248805,4	MCF-7	breast:

Variant related genes	Relation type
DNAH10	TF binding region
ENSG00000185344	Chromatin interaction
ENSG00000197653	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10082815	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10160842	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10160937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1040156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs1051793	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1060637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10734903	0.89[EUR][1000 genomes]
rs10734904	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10734905	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10734906	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10734908	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744157	0.86[EUR][1000 genomes]
rs10744158	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10744159	0.86[EUR][1000 genomes]
rs10744160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10744161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10744162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773026	0.86[EUR][1000 genomes]
rs10773030	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10773031	0.83[EUR][1000 genomes]
rs10773032	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10773033	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10773034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10846537	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10846549	0.92[EUR][1000 genomes]
rs10846550	0.92[EUR][1000 genomes]
rs10846551	0.83[EUR][1000 genomes]
rs10846553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1139789	0.89[EUR][1000 genomes]
rs11572920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11572952	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11609591	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611354	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612030	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612479	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612927	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11613632	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11837144	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12580486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs12817757	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12820195	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12827074	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12829893	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12830927	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1399961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1515815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1878077	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2176152	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2222060	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2271660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs2271661	0.93[EUR][1000 genomes]
rs2271662	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2333835	0.89[EUR][1000 genomes]
rs2333836	0.93[EUR][1000 genomes]
rs2333837	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2333838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs2333839	0.92[EUR][1000 genomes]
rs2333840	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs34247974	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930708	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488888	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6488893	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488897	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6488899	0.87[EUR][1000 genomes]
rs6488900	0.84[EUR][1000 genomes]
rs6488902	0.85[EUR][1000 genomes]
rs7132115	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7135660	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136939	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7137946	0.81[CEU][hapmap]
rs7139193	0.81[CEU][hapmap]
rs7294984	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7295552	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7297576	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298440	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298831	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7300721	0.92[EUR][1000 genomes]
rs7300818	0.86[EUR][1000 genomes]
rs7301641	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7302649	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7302708	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7306549	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7307008	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7307343	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7308398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7308862	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7309528	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7310918	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7311789	0.86[EUR][1000 genomes]
rs7313032	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7313261	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7397240	0.85[EUR][1000 genomes]
rs7397745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7397746	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7398082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs7398384	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7398606	0.87[EUR][1000 genomes]
rs7398641	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7398851	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7399128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7399224	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7953599	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7956045	0.84[EUR][1000 genomes]
rs7956751	0.86[EUR][1000 genomes]
rs7958693	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7959553	0.81[CEU][hapmap]
rs7960403	0.86[EUR][1000 genomes]
rs7963968	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7964443	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7966867	0.81[CEU][hapmap]
rs7973155	0.81[CEU][hapmap]
rs7973695	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7974279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7974331	0.86[EUR][1000 genomes]
rs7974462	0.86[EUR][1000 genomes]
rs7975119	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7975233	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7976110	0.85[AFR][1000 genomes]
rs7978447	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7979528	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs882563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs968203	0.86[EUR][1000 genomes]
rs9787987	0.89[EUR][1000 genomes]
rs9788204	0.86[AMR][1000 genomes];0.92[EUR][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	esv3389445	chr12:124245999-124247847	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2333834	ATP6V0A2	cis	Nerve Tibial	GTEx
rs2333834	TCTN2	cis	lung	GTEx
rs2333834	TCTN2	cis	Stomach	GTEx
rs2333834	TCTN2	cis	Adipose Subcutaneous	GTEx
rs2333834	DDX55	cis	Brain Pons	GTEx
rs2333834	TCTN2	cis	Artery Tibial	GTEx
rs2333834	TCTN2	cis	Thyroid	GTEx
rs2333834	TCTN2	cis	Nerve Tibial	GTEx
rs2333834	TCTN2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:116 , 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	chr12:124203800-124248000	Strong transcription	Dnd41	blood
3	chr12:124221800-124246200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:124224200-124246400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:124229800-124246400	Weak transcription	Psoas Muscle	Psoas
6	chr12:124232000-124246400	Weak transcription	NHDF-Ad	bronchial
7	chr12:124234200-124247400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:124234800-124246400	Weak transcription	Stomach Mucosa	stomach
9	chr12:124235000-124246200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:124235400-124246400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:124239600-124246200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:124239600-124246200	Weak transcription	NH-A	brain
13	chr12:124239800-124246200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:124239800-124246200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:124239800-124246200	Weak transcription	Brain Anterior Caudate	brain
16	chr12:124239800-124246200	Weak transcription	Colonic Mucosa	Colon
17	chr12:124239800-124246400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:124239800-124246400	Weak transcription	Aorta	Aorta
19	chr12:124239800-124246400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:124239800-124246400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:124239800-124246400	Weak transcription	HMEC	breast
22	chr12:124239800-124246800	Weak transcription	Brain Angular Gyrus	brain
23	chr12:124239800-124247200	Weak transcription	HSMM	muscle
24	chr12:124239800-124249400	Weak transcription	Brain Substantia Nigra	brain
25	chr12:124239800-124252000	Weak transcription	K562	blood
26	chr12:124240000-124246200	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:124240000-124246400	Weak transcription	Ovary	ovary
28	chr12:124241200-124246400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:124241200-124246400	Weak transcription	Small Intestine	intestine
30	chr12:124241400-124246400	Weak transcription	Pancreas	Pancrea
31	chr12:124241600-124246200	Weak transcription	Thymus	Thymus
32	chr12:124241600-124246400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:124241600-124246400	Weak transcription	Esophagus	oesophagus
34	chr12:124241600-124246400	Weak transcription	Gastric	stomach
35	chr12:124241800-124246200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:124241800-124246200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:124241800-124246200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:124242000-124246200	Weak transcription	A549	lung
39	chr12:124242400-124246200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:124242400-124246200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:124242400-124246200	Weak transcription	Right Ventricle	heart
42	chr12:124242400-124246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:124242400-124246400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:124242400-124246400	Weak transcription	Spleen	Spleen
45	chr12:124242600-124246200	Weak transcription	Adipose Nuclei	Adipose
46	chr12:124242600-124246400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:124242800-124246400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:124243200-124246400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:124243800-124246200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:124244600-124246200	Weak transcription	Primary T cells from cord blood	blood

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