Variant report

Variant	rs1716185
Chromosome Location	chr12:123638070-123638071
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123637916-123638328	K562	blood:	n/a	n/a
2	POLR2A	chr12:123635871-123638687	K562	blood:	n/a	n/a
3	POLR2A	chr12:123637805-123638302	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123517171..123520609-chr12:123634791..123638617,3	K562	blood:
2	chr12:123633613..123635147-chr12:123636492..123638541,2	MCF-7	breast:
3	chr12:123636212..123638464-chr12:123674064..123676672,2	K562	blood:
4	chr12:123635970..123638934-chr12:124084716..124087509,2	MCF-7	breast:
5	chr12:123635116..123639048-chr12:123716065..123719246,5	K562	blood:
6	chr12:123458168..123460396-chr12:123636633..123638279,2	K562	blood:
7	chr12:123637836..123642861-chr12:123644495..123649304,6	MCF-7	breast:

No data

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000090975	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1047158	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051431	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744147	0.91[EUR][1000 genomes]
rs10772993	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772995	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10772998	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10846478	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10846486	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057192	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057204	0.81[EUR][1000 genomes]
rs11057206	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11057210	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1106240	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106241	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260294	0.83[EUR][1000 genomes]
rs1402274	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1569068	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615350	0.81[EUR][1000 genomes]
rs1615694	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1616131	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616181	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617156	0.88[EUR][1000 genomes]
rs1617434	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618679	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621194	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626899	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1627724	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630693	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1630905	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716156	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716157	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716158	0.86[EUR][1000 genomes]
rs1716159	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716160	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716162	0.88[AMR][1000 genomes]
rs1716164	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716165	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716167	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716168	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716170	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716171	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716172	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1716173	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716175	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716176	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716177	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716182	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716183	0.93[ASN][1000 genomes]
rs1727290	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1727294	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1727296	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1727300	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727302	0.82[EUR][1000 genomes]
rs1727306	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727309	0.88[EUR][1000 genomes]
rs1727310	0.88[EUR][1000 genomes]
rs1727313	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727314	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727315	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727316	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727317	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727318	0.92[EUR][1000 genomes]
rs1727320	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1727322	0.84[EUR][1000 genomes]
rs1727323	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1727324	0.88[EUR][1000 genomes]
rs1727325	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1727334	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1790086	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1790087	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1790089	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1790090	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790095	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1790098	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1790100	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1790101	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790102	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790108	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790109	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790116	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790119	0.82[EUR][1000 genomes]
rs1790120	0.87[EUR][1000 genomes]
rs1790123	0.88[EUR][1000 genomes]
rs1790124	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790125	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790130	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790131	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2049114	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2510885	0.93[EUR][1000 genomes]
rs2682425	0.82[EUR][1000 genomes]
rs2682426	0.81[AMR][1000 genomes]
rs2682429	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682430	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2682431	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682433	0.89[EUR][1000 genomes]
rs2682434	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2695476	0.89[EUR][1000 genomes]
rs2695478	0.90[EUR][1000 genomes]
rs2695479	0.88[EUR][1000 genomes]
rs2695480	0.87[EUR][1000 genomes]
rs2695481	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695482	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851435	0.87[EUR][1000 genomes]
rs2851436	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2851438	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851441	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851450	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2851451	0.90[EUR][1000 genomes]
rs2947099	0.89[EUR][1000 genomes]
rs2950537	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3018098	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4372492	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4759409	0.82[AMR][1000 genomes]
rs884548	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941305	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs941306	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs949142	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9795522	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1716185	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1716185	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1716185	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1716185	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1716185	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1716185	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1716185	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636400-123639800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:123636400-123640000	Weak transcription	K562	blood
3	chr12:123636400-123640400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:123636400-123644600	Weak transcription	GM12878-XiMat	blood
5	chr12:123636400-123648000	Weak transcription	Fetal Kidney	kidney
6	chr12:123636400-123649000	Weak transcription	Small Intestine	intestine
7	chr12:123636400-123649200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:123636400-123649800	Weak transcription	Ovary	ovary
9	chr12:123636400-123650200	Weak transcription	Aorta	Aorta
10	chr12:123636600-123638400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123636600-123638400	Weak transcription	Brain Germinal Matrix	brain
12	chr12:123636600-123639800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:123636600-123640000	Weak transcription	HSMM	muscle
14	chr12:123636600-123640200	Weak transcription	Fetal Brain Female	brain
15	chr12:123636600-123640400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:123636600-123644600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:123636600-123644800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:123636600-123644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:123636600-123645000	Weak transcription	NH-A	brain
20	chr12:123636600-123645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:123636600-123645200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:123636600-123645200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:123636600-123647000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:123636600-123647000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:123636600-123647400	Weak transcription	HMEC	breast
26	chr12:123636600-123647600	Weak transcription	NHEK	skin
27	chr12:123636600-123648400	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:123636600-123648400	Weak transcription	HSMMtube	muscle
29	chr12:123636600-123660800	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:123636600-123676200	Weak transcription	Gastric	stomach
31	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
32	chr12:123636800-123638400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:123636800-123639000	Weak transcription	NHLF	lung
34	chr12:123636800-123639200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:123636800-123639200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:123636800-123639600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:123636800-123639800	Weak transcription	Left Ventricle	heart
38	chr12:123636800-123639800	Weak transcription	HUVEC	blood vessel
39	chr12:123636800-123639800	Weak transcription	Osteobl	bone
40	chr12:123636800-123640000	Weak transcription	Primary T cells from cord blood	blood
41	chr12:123636800-123640000	Weak transcription	A549	lung
42	chr12:123636800-123640200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:123636800-123640200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:123636800-123643200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:123636800-123644200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:123636800-123645200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:123636800-123645200	Weak transcription	NHDF-Ad	bronchial
48	chr12:123636800-123646200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:123636800-123646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:123636800-123647200	Weak transcription	Rectal Mucosa Donor 31	rectum

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