Variant report

Variant	rs949143
Chromosome Location	chr12:123595163-123595164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123595122-123595172	GM12878	blood:	n/a
2	chr12:123595122-123595172	HPAEpiC	pulmonary alveolar:	n/a
3	chr12:123595122-123595172	Hepatocyte	liver:	n/a
4	chr12:123595122-123595172	NH-A	brain:	n/a
5	chr12:123595122-123595172	GM19239	blood:	n/a
6	chr12:123595122-123595172	HepG2	liver:	n/a
7	chr12:123595122-123595172	K562	blood:	n/a
8	chr12:123595122-123595172	GM06990	blood:	n/a
9	chr12:123595122-123595172	HRCEpiC	kidney:	n/a
10	chr12:123595122-123595172	Hela-S3	cervix:	n/a
11	chr12:123595122-123595172	SK-N-SH_RA	brain:	n/a
12	chr12:123595122-123595172	HRPEpiC	eye:	n/a
13	chr12:123595122-123595172	HAEpiC	amniotic membrane:	n/a
14	chr12:123595122-123595172	PFSK-1	brain:	n/a
15	chr12:123595122-123595172	HCF	heart:	n/a
16	chr12:123595122-123595172	HMEC	breast:	n/a
17	chr12:123595122-123595172	NB4	blood:	n/a
18	chr12:123595122-123595172	SAEC	small airway:	n/a
19	chr12:123595122-123595172	U87	brain:	n/a
20	chr12:123595122-123595172	MCF10A-Er-Src	breast:	n/a
21	chr12:123595122-123595172	NHDF-neo	bronchial:	n/a
22	chr12:123595122-123595172	PrEC	prostate:	n/a
23	chr12:123595122-123595172	ovcar-3	ovarian:	n/a
24	chr12:123595122-123595172	HCM	heart:	n/a
25	chr12:123595122-123595172	AG04450	lung:	fetal
26	chr12:123595122-123595172	IMR90	lung:	fetal
27	chr12:123595122-123595172	AG09319	gingival:	n/a
28	chr12:123595122-123595172	NHBE	bronchial:	n/a
29	chr12:123595122-123595172	SKMC	muscle:	n/a
30	chr12:123595122-123595172	AoSMC	blood vessel:	n/a
31	chr12:123595122-123595172	HIPEpiC	eye:	n/a
32	chr12:123595122-123595172	RPTEC	kidney:	n/a
33	chr12:123595122-123595172	Caco-2	colon:	n/a
34	chr12:123595122-123595172	AG10803	skin:	n/a
35	chr12:123595122-123595172	HRE	kidney:	n/a
36	chr12:123595122-123595172	SK-N-SH	brain:	n/a
37	chr12:123595122-123595172	T-47D	breast:	n/a
38	chr12:123595122-123595172	HEEpiC	esophagus:	n/a
39	chr12:123595122-123595172	HL-60	blood:	n/a
40	chr12:123595122-123595172	AG04449	skin:	fetal
41	chr12:123595122-123595172	HCT-116	colon:	n/a
42	chr12:123595122-123595172	SK-N-MC	brain:	n/a
43	chr12:123595122-123595172	MCF-7	breast:	n/a
44	chr12:123595122-123595172	HCPEpiC	choroid plexus:	n/a
45	chr12:123595122-123595172	LNCaP	prostate:	n/a
46	chr12:123595122-123595172	BE2_C	brain:	n/a
47	chr12:123595122-123595172	HUVEC	blood vessel:	n/a
48	chr12:123595122-123595172	GM12891	blood:	n/a
49	chr12:123595122-123595172	HNPCEpiC	eye:	n/a
50	chr12:123595122-123595172	Jurkat	blood:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123593239..123596148-chr12:123716066..123718804,3	K562	blood:
2	chr12:123589646..123591494-chr12:123593029..123596172,4	K562	blood:

No data

Variant related genes	Relation type
PITPNM2	CpG island
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10773002	0.83[ASW][hapmap]
rs10773003	0.80[JPT][hapmap]
rs10773005	0.80[JPT][hapmap]
rs10773921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846489	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs10848428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057251	0.90[ASW][hapmap];0.80[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11060853	0.81[JPT][hapmap]
rs1109559	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11608305	0.80[JPT][hapmap]
rs11608811	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11610710	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11613937	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12229700	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12317452	0.80[JPT][hapmap]
rs12425009	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1568427	0.83[ASW][hapmap]
rs1568428	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs1611973	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1615350	0.83[ASW][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1626703	0.84[AFR][1000 genomes]
rs1716178	0.82[AMR][1000 genomes]
rs1716184	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727286	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727293	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727295	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1727301	0.85[JPT][hapmap]
rs1727302	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1727305	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1727307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727312	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790088	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790094	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790096	0.84[AFR][1000 genomes]
rs1790104	0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1790106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790121	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790122	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790129	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1790134	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1879379	1.00[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1984658	0.81[EUR][1000 genomes]
rs2682427	0.85[JPT][hapmap]
rs28755851	0.80[EUR][1000 genomes]
rs3088303	0.80[JPT][hapmap]
rs3741530	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3759115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3897102	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4148862	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4148863	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4275659	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs585522	0.80[GIH][hapmap]
rs7135296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7139321	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs7304782	0.83[ASW][hapmap]
rs7305511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884956	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs940904	0.80[GIH][hapmap]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs949143	PITPNM2	cis	cerebellum	SCAN
rs949143	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs949143	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs949143	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs949143	TMEM120B	cis	parietal	SCAN
rs949143	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs949143	C12orf65	cis	cerebellum	SCAN
rs949143	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs949143	CDK2AP1	cis	cerebellum	SCAN
rs949143	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 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	chr12:123579800-123596200	Weak transcription	Osteobl	bone
4	chr12:123580600-123596000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123583000-123595800	Weak transcription	NHDF-Ad	bronchial
6	chr12:123583200-123599600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:123587200-123595600	Enhancers	Liver	Liver
8	chr12:123588000-123599000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:123589400-123595400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:123589600-123595200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr12:123590000-123595200	Strong transcription	Fetal Intestine Small	intestine
12	chr12:123590000-123596600	Enhancers	Right Ventricle	heart
13	chr12:123590000-123598200	Enhancers	Right Atrium	heart
14	chr12:123590000-123603800	Enhancers	Left Ventricle	heart
15	chr12:123590600-123596000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:123590600-123598800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:123591000-123599400	Enhancers	Brain Anterior Caudate	brain
18	chr12:123591200-123595200	Strong transcription	Fetal Stomach	stomach
19	chr12:123591200-123597000	Genic enhancers	Stomach Smooth Muscle	stomach
20	chr12:123591600-123595800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:123591800-123596200	Weak transcription	Esophagus	oesophagus
22	chr12:123592000-123595600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:123592000-123596200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:123592000-123596400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:123592000-123599000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:123592000-123599800	Weak transcription	HMEC	breast
27	chr12:123592200-123595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:123592200-123595800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:123592200-123596000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:123592200-123596200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:123592200-123597400	Weak transcription	A549	lung
32	chr12:123592200-123599200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:123592200-123600200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:123592200-123601000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:123592400-123596000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:123592400-123596000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:123592400-123598400	Weak transcription	HUVEC	blood vessel
38	chr12:123592400-123598600	Weak transcription	Fetal Lung	lung
39	chr12:123592400-123601000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:123592600-123595800	Weak transcription	K562	blood
41	chr12:123592600-123596400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:123592600-123596400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:123592600-123598800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:123592800-123595200	Genic enhancers	Lung	lung
45	chr12:123592800-123595600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr12:123592800-123611200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:123593000-123595200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:123593000-123595200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:123593000-123595200	Enhancers	Brain Substantia Nigra	brain
50	chr12:123593000-123595600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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