Variant report

Variant	rs940904
Chromosome Location	chr12:123491572-123491573
allele	A/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	MAFK	chr12:123491567-123491801	HepG2	liver:	n/a	n/a
2	MAFK	chr12:123491454-123491811	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123491404..123492960-chr12:123494344..123496254,2	K562	blood:
2	chr12:123490178..123492960-chr12:123494344..123496225,2	K562	blood:

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000265526	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10773921	0.80[GIH][hapmap]
rs10848428	0.80[GIH][hapmap]
rs11608811	0.80[GIH][hapmap]
rs12820906	0.80[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1463877	0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1617156	0.93[ASW][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap]
rs1727307	0.80[GIH][hapmap]
rs1790094	0.80[GIH][hapmap]
rs1790106	0.80[GIH][hapmap]
rs1790121	0.80[GIH][hapmap]
rs2270789	0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs4148856	0.82[ASN][1000 genomes]
rs4148863	0.80[GIH][hapmap]
rs520088	0.93[ASW][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap]
rs585522	0.93[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs641760	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs655293	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs7299943	0.86[ASW][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs883263	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs883563	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937564	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949143	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	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
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	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
8	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs940904	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs940904	ANAPC5	cis	parietal	SCAN
rs940904	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs940904	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs940904	TMEM120B	cis	parietal	SCAN
rs940904	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs940904	CDK2AP1	cis	lesional skin	skin_eQTL
rs940904	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs940904	PITPNM2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
2	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
3	chr12:123469200-123498600	Strong transcription	Primary T cells from cord blood	blood
4	chr12:123469400-123491600	Weak transcription	HMEC	breast
5	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
6	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:123469800-123491600	Weak transcription	Osteobl	bone
9	chr12:123470200-123512800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
11	chr12:123472000-123499000	Strong transcription	Thymus	Thymus
12	chr12:123472600-123492800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:123472800-123494200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:123472800-123500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:123473400-123501000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:123473800-123492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:123473800-123500800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:123481400-123491800	Weak transcription	HepG2	liver
19	chr12:123481800-123492600	Weak transcription	Primary B cells from cord blood	blood
20	chr12:123483200-123496800	Weak transcription	Psoas Muscle	Psoas
21	chr12:123484400-123492800	Weak transcription	Brain Substantia Nigra	brain
22	chr12:123485200-123496200	Strong transcription	Fetal Thymus	thymus
23	chr12:123485600-123495600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:123485800-123493200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:123486000-123491800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:123487400-123497600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:123487600-123498800	Strong transcription	Fetal Stomach	stomach
28	chr12:123488000-123497400	Strong transcription	Ovary	ovary
29	chr12:123488000-123498400	Strong transcription	Right Ventricle	heart
30	chr12:123488000-123498800	Strong transcription	Fetal Intestine Small	intestine
31	chr12:123488200-123494200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:123488400-123498600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:123488600-123498600	Strong transcription	Liver	Liver
34	chr12:123488800-123492000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:123488800-123498400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:123489200-123512400	Weak transcription	Aorta	Aorta
37	chr12:123489400-123492600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:123489800-123491800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:123489800-123492200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:123489800-123492600	Weak transcription	Fetal Brain Female	brain
41	chr12:123489800-123492800	Weak transcription	Brain Germinal Matrix	brain
42	chr12:123490000-123491600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:123490000-123491600	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:123490000-123491600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:123490000-123491800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:123490000-123493400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:123490000-123494000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:123490000-123495600	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:123490000-123515800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:123490200-123491600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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