Variant report

Variant	rs937564
Chromosome Location	chr12:123477311-123477312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123476420..123479268-chr12:123480429..123483932,4	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1051431	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1106240	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1106241	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1260294	1.00[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs12811109	0.96[EUR][1000 genomes]
rs12820906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12828755	0.96[EUR][1000 genomes]
rs1463877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1569068	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1615350	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1617156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs1716157	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716164	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716165	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716167	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716168	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716175	0.94[CEU][hapmap]
rs1716176	0.94[CEU][hapmap]
rs1716177	0.94[CEU][hapmap]
rs1727294	0.93[CEU][hapmap]
rs1727296	0.94[CEU][hapmap]
rs1727302	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1727306	0.94[CEU][hapmap]
rs1727309	0.94[CEU][hapmap];0.91[TSI][hapmap]
rs1727313	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1727315	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1790098	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1790100	0.94[CEU][hapmap]
rs1790108	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1790116	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs1790123	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs2049114	0.94[CEU][hapmap]
rs2270789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2695482	0.94[CEU][hapmap]
rs2851447	0.82[CEU][hapmap]
rs4148856	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs520088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs585522	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs641760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs655293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7132277	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs71444568	0.88[EUR][1000 genomes]
rs7296418	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs7299943	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]
rs883263	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883563	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs884548	0.94[CEU][hapmap]
rs940904	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]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv560493	chr12:123467325-123479623	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs937564	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs937564	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs937564	PITPNM2	cis	cerebellum	SCAN
rs937564	WDR66	cis	parietal	SCAN
rs937564	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs937564	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs937564	ANAPC5	cis	parietal	SCAN
rs937564	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs937564	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs937564	CCDC92	cis	cerebellum	SCAN
rs937564	CDK2AP1	cis	lymphoblastoid	seeQTL
rs937564	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs937564	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs937564	TMEM120B	cis	parietal	SCAN
rs937564	HIP1R	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123466600-123483400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
3	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
4	chr12:123468000-123486200	Strong transcription	Fetal Brain Female	brain
5	chr12:123468200-123477800	Strong transcription	Brain Germinal Matrix	brain
6	chr12:123468800-123485200	Weak transcription	Aorta	Aorta
7	chr12:123469200-123477400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:123469200-123498600	Strong transcription	Primary T cells from cord blood	blood
9	chr12:123469400-123479400	Weak transcription	Psoas Muscle	Psoas
10	chr12:123469400-123491600	Weak transcription	HMEC	breast
11	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
12	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:123469600-123484600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:123469800-123485800	Strong transcription	Placenta	Placenta
16	chr12:123469800-123486800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:123469800-123491400	Weak transcription	HSMMtube	muscle
18	chr12:123469800-123491600	Weak transcription	Osteobl	bone
19	chr12:123470000-123480000	Weak transcription	Right Atrium	heart
20	chr12:123470000-123486200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:123470000-123486200	Weak transcription	HSMM	muscle
22	chr12:123470000-123486600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:123470200-123479200	Strong transcription	Fetal Thymus	thymus
24	chr12:123470200-123479800	Strong transcription	Right Ventricle	heart
25	chr12:123470200-123480400	Weak transcription	HepG2	liver
26	chr12:123470200-123512800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:123470400-123480000	Strong transcription	Left Ventricle	heart
28	chr12:123470400-123482800	Strong transcription	Gastric	stomach
29	chr12:123470400-123483600	Weak transcription	Brain Substantia Nigra	brain
30	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
31	chr12:123470600-123478800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:123470600-123486200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:123471000-123478200	Strong transcription	Brain Anterior Caudate	brain
34	chr12:123471600-123484600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:123472000-123499000	Strong transcription	Thymus	Thymus
36	chr12:123472200-123484200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:123472400-123477600	Strong transcription	Spleen	Spleen
38	chr12:123472400-123480800	Weak transcription	NHEK	skin
39	chr12:123472400-123491400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:123472600-123492800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:123472800-123494200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:123472800-123500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:123473000-123479000	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:123473000-123484400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:123473200-123480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:123473200-123481400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:123473200-123483800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:123473200-123484200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:123473200-123489400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:123473200-123489400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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