Variant report

Variant	rs12366410
Chromosome Location	chr12:48066216-48066217
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48058363..48062042-chr12:48064816..48068792,4	K562	blood:
2	chr12:48059314..48062042-chr12:48063084..48066316,3	K562	blood:
3	chr12:48064589..48067295-chr12:48089738..48092390,2	K562	blood:

Variant related genes	Relation type
ENSG00000005175	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10783212	0.97[ASN][1000 genomes]
rs10875677	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875682	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875685	0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875686	0.83[ASN][1000 genomes]
rs10875687	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875688	0.81[ASN][1000 genomes]
rs11168191	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168193	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168200	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168203	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168208	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168214	0.81[ASN][1000 genomes]
rs11168215	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168216	0.81[ASN][1000 genomes]
rs12367193	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12370643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1541384	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072117	0.81[ASN][1000 genomes]
rs2240079	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2240080	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs2283346	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764013	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs56011001	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56240307	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582680	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583752	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs602143	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs604662	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs605499	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs611627	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs612773	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61917590	0.92[ASN][1000 genomes]
rs61917591	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61917594	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61917595	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61917616	0.81[ASN][1000 genomes]
rs61917617	0.81[ASN][1000 genomes]
rs622098	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs623894	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs630777	0.93[ASN][1000 genomes]
rs632944	0.93[ASN][1000 genomes]
rs634833	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs642453	0.83[EUR][1000 genomes]
rs644531	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs646223	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs652380	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs653136	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6580634	0.96[ASN][1000 genomes]
rs658567	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs659836	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs668968	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs671961	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs679789	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs687676	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7136561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137529	0.94[ASN][1000 genomes]
rs7311663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7316761	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7484827	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs7954502	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968783	0.80[AMR][1000 genomes]
rs7969186	0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7976748	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7977613	1.00[ASN][1000 genomes]
rs7977786	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs864112	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12366410	RPAP3	cis	cerebellum	SCAN
rs12366410	YAF2	cis	cerebellum	SCAN
rs12366410	ENDOU	cis	Thyroid	GTEx
rs12366410	DNAJC22	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:48031000-48083200	Weak transcription	Esophagus	oesophagus
3	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
4	chr12:48043400-48080000	Weak transcription	NHEK	skin
5	chr12:48045200-48079200	Weak transcription	NHLF	lung
6	chr12:48046200-48068000	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:48046600-48083000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
10	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:48046600-48099200	Weak transcription	Gastric	stomach
13	chr12:48046800-48079200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:48046800-48083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:48050200-48098600	Weak transcription	Pancreas	Pancrea
18	chr12:48051400-48069200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:48051800-48069400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:48052000-48094400	Weak transcription	Aorta	Aorta
21	chr12:48053000-48068600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:48053600-48067000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:48055200-48083200	Weak transcription	Brain Germinal Matrix	brain
24	chr12:48056000-48073000	Weak transcription	Fetal Brain Female	brain
25	chr12:48056000-48075000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
27	chr12:48057200-48067000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:48057200-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:48058000-48098600	Weak transcription	Colonic Mucosa	Colon
30	chr12:48058200-48067200	Strong transcription	Primary B cells from cord blood	blood
31	chr12:48058200-48069000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:48058200-48086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:48058400-48066800	Strong transcription	A549	lung
34	chr12:48058600-48070000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:48058600-48082600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:48058800-48067800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:48058800-48071600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:48058800-48086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:48059000-48069400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:48059800-48068200	Strong transcription	HSMM	muscle
41	chr12:48059800-48083000	Weak transcription	Fetal Intestine Small	intestine
42	chr12:48059800-48083200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:48060000-48066400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:48060200-48066400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:48060400-48083000	Weak transcription	Spleen	Spleen
46	chr12:48060400-48088400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:48060600-48067600	Weak transcription	Left Ventricle	heart
48	chr12:48060600-48067800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:48060600-48067800	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:48060600-48072800	Weak transcription	Ovary	ovary

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