Variant report

Variant	rs7299943
Chromosome Location	chr12:123593485-123593486
allele	A/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	MAX	chr12:123593340-123593625	NB4	blood:	n/a	chr12:123593486-123593496
2	MAX	chr12:123593361-123593646	K562	blood:	n/a	chr12:123593486-123593496

No.	Distal block	Cell Line	Cell type
1	chr12:123593239..123596148-chr12:123716066..123718804,3	K562	blood:
2	chr12:123587888..123589723-chr12:123591389..123594363,2	MCF-7	breast:
3	chr12:123589646..123591494-chr12:123593029..123596172,4	K562	blood:

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000090975	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1047158	0.80[EUR][1000 genomes]
rs1051431	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs10772998	0.84[CEU][hapmap]
rs10846486	0.89[CEU][hapmap]
rs11057192	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs1106240	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs1106241	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1260294	0.94[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs12817892	0.91[CEU][hapmap]
rs12820906	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1402274	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1463877	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs1533703	0.81[CEU][hapmap]
rs1569068	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1616131	0.82[EUR][1000 genomes]
rs1616181	0.82[EUR][1000 genomes]
rs1617156	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627724	0.80[EUR][1000 genomes]
rs1716157	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs1716160	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1716164	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs1716165	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1716167	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1716168	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1716170	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs1716171	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs1716175	0.89[CEU][hapmap]
rs1716176	0.89[CEU][hapmap]
rs1716177	0.89[CEU][hapmap]
rs1727294	0.87[CEU][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727296	0.89[CEU][hapmap]
rs1727306	0.89[CEU][hapmap]
rs1727309	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs1727313	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs1727315	0.89[CEU][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1727316	0.82[EUR][1000 genomes]
rs1727320	0.89[CEU][hapmap]
rs1727323	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1727324	0.89[CEU][hapmap]
rs1727325	0.89[CEU][hapmap]
rs1790090	0.80[EUR][1000 genomes]
rs1790095	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs1790098	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs1790100	0.89[CEU][hapmap]
rs1790108	0.89[CEU][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs1790109	0.80[EUR][1000 genomes]
rs1790116	0.82[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1790119	0.85[ASN][1000 genomes]
rs1790120	0.92[ASN][1000 genomes]
rs1790123	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs1790131	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1879380	0.89[CEU][hapmap]
rs1969354	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1980252	0.84[CEU][hapmap]
rs2049114	0.89[CEU][hapmap]
rs2270789	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2337934	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2510885	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682429	0.80[EUR][1000 genomes]
rs2682434	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs2695478	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2695481	0.80[EUR][1000 genomes]
rs2695482	0.89[CEU][hapmap]
rs2851438	0.80[EUR][1000 genomes]
rs4372492	0.89[CEU][hapmap]
rs4759371	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs4759409	0.84[CEU][hapmap]
rs4759415	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs520088	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs585522	0.93[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs641760	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs655293	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7132277	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs71444568	0.92[ASN][1000 genomes]
rs7296418	0.81[MEX][hapmap]
rs7313483	0.84[CEU][hapmap]
rs7953929	0.89[CEU][hapmap]
rs7975763	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883263	0.92[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs884548	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs937564	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs940904	0.86[ASW][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs941305	0.89[CEU][hapmap]
rs941306	0.89[CEU][hapmap]
rs949142	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7299943	MPHOSPH9	cis	multi-tissue	Pritchard
rs7299943	TMEM120B	cis	parietal	SCAN
rs7299943	ANAPC5	cis	parietal	SCAN
rs7299943	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs7299943	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs7299943	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs7299943	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs7299943	PITPNM2	cis	cerebellum	SCAN
rs7299943	ARL6IP4	cis	lymphoblastoid	seeQTL
rs7299943	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs7299943	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs7299943	HIP1R	cis	parietal	SCAN
rs7299943	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs7299943	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs7299943	DNAH10	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
2	chr12:123571200-123600000	Genic enhancers	Thymus	Thymus
3	chr12:123579800-123593600	Weak transcription	Fetal Intestine Large	intestine
4	chr12:123579800-123596200	Weak transcription	Osteobl	bone
5	chr12:123580000-123593800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:123580600-123596000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:123583000-123595800	Weak transcription	NHDF-Ad	bronchial
8	chr12:123583200-123599600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:123587200-123595600	Enhancers	Liver	Liver
10	chr12:123588000-123599000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:123589400-123594200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:123589400-123595400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:123589600-123593600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:123589600-123595200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:123590000-123593800	Enhancers	Fetal Heart	heart
16	chr12:123590000-123595200	Strong transcription	Fetal Intestine Small	intestine
17	chr12:123590000-123596600	Enhancers	Right Ventricle	heart
18	chr12:123590000-123598200	Enhancers	Right Atrium	heart
19	chr12:123590000-123603800	Enhancers	Left Ventricle	heart
20	chr12:123590400-123594400	Enhancers	Adipose Nuclei	Adipose
21	chr12:123590600-123594400	Enhancers	Spleen	Spleen
22	chr12:123590600-123596000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:123590600-123598800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:123591000-123594000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:123591000-123599400	Enhancers	Brain Anterior Caudate	brain
26	chr12:123591200-123594000	Genic enhancers	Brain Angular Gyrus	brain
27	chr12:123591200-123594400	Enhancers	Brain Hippocampus Middle	brain
28	chr12:123591200-123595200	Strong transcription	Fetal Stomach	stomach
29	chr12:123591200-123597000	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr12:123591600-123595800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:123591800-123593800	Enhancers	HSMMtube	muscle
32	chr12:123591800-123596200	Weak transcription	Esophagus	oesophagus
33	chr12:123592000-123593600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:123592000-123593600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:123592000-123594000	Genic enhancers	Primary T cells from cord blood	blood
36	chr12:123592000-123594200	Strong transcription	NHLF	lung
37	chr12:123592000-123595600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:123592000-123596200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:123592000-123596400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:123592000-123599000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:123592000-123599800	Weak transcription	HMEC	breast
42	chr12:123592200-123593600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:123592200-123593600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:123592200-123593800	Genic enhancers	Hela-S3	cervix
45	chr12:123592200-123594400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr12:123592200-123595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:123592200-123595800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:123592200-123596000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:123592200-123596200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:123592200-123597400	Weak transcription	A549	lung

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