Variant report

Variant	rs2851447
Chromosome Location	chr12:123665113-123665114
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123664973..123667049-chr12:123717429..123718943,2	K562	blood:

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1051431	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10732573	0.89[CEU][hapmap]
rs10744150	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10744151	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10772993	0.81[EUR][1000 genomes]
rs10772995	0.83[EUR][1000 genomes]
rs10772997	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10772998	0.88[CEU][hapmap]
rs10772999	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10773002	0.84[CEU][hapmap]
rs10846478	0.83[EUR][1000 genomes]
rs10846486	0.88[CEU][hapmap]
rs11057189	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11057192	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11057202	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11057205	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11057207	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11057209	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1106240	0.88[CEU][hapmap]
rs1106241	0.88[CEU][hapmap]
rs11610710	0.80[EUR][1000 genomes]
rs12229700	0.81[EUR][1000 genomes]
rs12298826	0.82[CEU][hapmap]
rs12316131	0.82[CEU][hapmap]
rs12322888	0.82[CEU][hapmap]
rs1260294	0.82[CEU][hapmap]
rs12817892	0.83[CEU][hapmap]
rs1402274	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1463877	0.82[CEU][hapmap]
rs1533703	0.81[CEU][hapmap]
rs1569068	0.88[CEU][hapmap]
rs1609520	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1615350	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1615694	0.82[EUR][1000 genomes]
rs1617156	0.82[CEU][hapmap]
rs1621194	0.81[EUR][1000 genomes]
rs1626899	0.81[EUR][1000 genomes]
rs1630693	0.82[EUR][1000 genomes]
rs1630905	0.82[EUR][1000 genomes]
rs1716157	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1716159	0.83[EUR][1000 genomes]
rs1716160	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1716164	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1716165	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1716167	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1716168	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1716170	0.88[CEU][hapmap]
rs1716171	0.88[CEU][hapmap]
rs1716175	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1716176	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1716177	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1716180	0.82[AMR][1000 genomes]
rs1716182	0.81[EUR][1000 genomes]
rs1727286	0.82[EUR][1000 genomes]
rs1727290	0.84[EUR][1000 genomes]
rs1727294	0.86[CEU][hapmap]
rs1727296	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1727300	0.81[EUR][1000 genomes]
rs1727302	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727306	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1727309	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1727310	0.81[EUR][1000 genomes]
rs1727313	0.88[CEU][hapmap]
rs1727315	0.88[CEU][hapmap]
rs1727319	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1727320	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1727323	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1727324	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1727325	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1727331	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1727332	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1727334	0.86[CEU][hapmap]
rs1790086	0.83[EUR][1000 genomes]
rs1790087	0.83[EUR][1000 genomes]
rs1790089	0.84[EUR][1000 genomes]
rs1790095	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1790098	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1790100	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1790101	0.82[EUR][1000 genomes]
rs1790102	0.82[EUR][1000 genomes]
rs1790108	0.88[CEU][hapmap]
rs1790116	0.82[CEU][hapmap]
rs1790123	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1790129	0.80[EUR][1000 genomes]
rs1790130	0.84[EUR][1000 genomes]
rs1790131	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1879380	0.88[CEU][hapmap]
rs1969354	0.82[CEU][hapmap]
rs1980252	0.82[CEU][hapmap]
rs2049114	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2102949	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2337934	0.82[CEU][hapmap]
rs2682430	0.81[EUR][1000 genomes]
rs2682431	0.83[EUR][1000 genomes]
rs2682433	0.81[EUR][1000 genomes]
rs2682434	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2695476	0.81[EUR][1000 genomes]
rs2695478	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2695479	0.81[EUR][1000 genomes]
rs2695482	0.88[CEU][hapmap]
rs28362667	0.81[ASN][1000 genomes]
rs28458312	0.82[CEU][hapmap]
rs2851436	0.81[EUR][1000 genomes]
rs2851443	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851450	0.83[EUR][1000 genomes]
rs2851451	0.82[EUR][1000 genomes]
rs2947099	0.81[EUR][1000 genomes]
rs3018098	0.84[EUR][1000 genomes]
rs36121382	0.87[ASN][1000 genomes]
rs3759111	0.89[ASN][1000 genomes]
rs3759113	0.94[ASN][1000 genomes]
rs4372492	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4460848	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759367	0.93[ASN][1000 genomes]
rs4759371	0.82[CEU][hapmap]
rs4759406	0.91[ASN][1000 genomes]
rs4759407	0.89[ASN][1000 genomes]
rs4759408	0.82[ASN][1000 genomes]
rs4759409	0.82[CEU][hapmap]
rs4759415	0.82[CEU][hapmap]
rs520088	0.82[CEU][hapmap]
rs57676984	0.82[ASN][1000 genomes]
rs58991895	0.90[ASN][1000 genomes]
rs60077920	0.82[ASN][1000 genomes]
rs60296110	0.91[ASN][1000 genomes]
rs61041384	0.91[ASN][1000 genomes]
rs61187102	0.90[ASN][1000 genomes]
rs641760	0.82[CEU][hapmap]
rs655293	0.82[CEU][hapmap]
rs7137286	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7304782	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7313483	0.88[CEU][hapmap]
rs7953929	0.88[CEU][hapmap]
rs883263	0.81[CEU][hapmap]
rs884548	0.88[CEU][hapmap]
rs937564	0.82[CEU][hapmap]
rs941305	0.88[CEU][hapmap]
rs941306	0.88[CEU][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	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
2	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
3	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
4	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
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2851447	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs2851447	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs2851447	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs2851447	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs2851447	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs2851447	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123676200	Weak transcription	Gastric	stomach
2	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
3	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
4	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
5	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
6	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
11	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
13	chr12:123648800-123673600	Weak transcription	HMEC	breast
14	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:123650600-123671600	Weak transcription	Brain Germinal Matrix	brain
16	chr12:123650600-123673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
18	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
19	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:123651200-123670000	Weak transcription	Spleen	Spleen
21	chr12:123651200-123673600	Weak transcription	Brain Substantia Nigra	brain
22	chr12:123651400-123672000	Weak transcription	NHDF-Ad	bronchial
23	chr12:123651400-123673600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:123651400-123673600	Weak transcription	NHEK	skin
25	chr12:123651400-123675800	Weak transcription	Ovary	ovary
26	chr12:123651600-123676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:123652000-123673000	Weak transcription	Aorta	Aorta
28	chr12:123652200-123676200	Weak transcription	Right Ventricle	heart
29	chr12:123652400-123665600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:123652600-123672800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:123653600-123666000	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:123653600-123666200	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:123654000-123707000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:123654400-123666600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:123654600-123666000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:123654600-123683000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:123655000-123666400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:123655000-123666400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:123655000-123666400	Strong transcription	Primary T cells from cord blood	blood
43	chr12:123655000-123666800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:123655000-123681000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:123655000-123707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:123655000-123708000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:123655200-123666200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr12:123655200-123666600	Strong transcription	Dnd41	blood
50	chr12:123655200-123682200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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