Variant report

Variant	rs10843822
Chromosome Location	chr12:30879088-30879089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:30876314..30879121-chr12:30906276..30907809,2	K562	blood:
2	chr12:30874193..30876323-chr12:30878456..30880055,2	MCF-7	breast:
3	chr12:30847240..30850434-chr12:30877265..30880526,5	K562	blood:

Variant related genes	Relation type
ENSG00000110888	Chromatin interaction
ENSG00000133704	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10444423	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10734793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743729	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10771756	0.83[ASN][1000 genomes]
rs10771757	0.85[ASN][1000 genomes]
rs10771760	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771762	0.93[ASN][1000 genomes]
rs10771768	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10843804	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10843813	0.81[ASN][1000 genomes]
rs10843814	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843815	0.93[ASN][1000 genomes]
rs10843816	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10843817	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10843818	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843819	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843820	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843823	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843824	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843829	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843831	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843832	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843833	0.89[JPT][hapmap]
rs10843834	0.91[ASN][1000 genomes]
rs10843835	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11051005	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11051010	0.80[ASN][1000 genomes]
rs11051027	0.85[ASN][1000 genomes]
rs11051045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051048	0.93[ASN][1000 genomes]
rs11051049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051050	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs11051053	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11051061	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs11051063	0.87[ASN][1000 genomes]
rs11835180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146709	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12303852	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12320609	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12368923	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369125	0.80[ASN][1000 genomes]
rs12370947	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12809335	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12809355	0.85[ASN][1000 genomes]
rs12825440	0.82[ASN][1000 genomes]
rs12826615	0.82[ASN][1000 genomes]
rs12830910	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2241828	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2289302	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2304630	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs35133495	0.94[ASN][1000 genomes]
rs35336533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4082413	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4335626	0.82[ASN][1000 genomes]
rs59177896	0.82[ASN][1000 genomes]
rs61923728	0.94[ASN][1000 genomes]
rs6487928	0.86[ASN][1000 genomes]
rs6487933	0.85[CHB][hapmap]
rs6487934	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487939	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7299800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304221	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7952744	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7955804	0.82[ASN][1000 genomes]
rs7957141	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7958274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958276	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966063	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7971762	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7971870	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7979718	0.82[ASN][1000 genomes]
rs7980510	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10843822	FLJ13224	cis	cerebellum	SCAN
rs10843822	IPO8	cis	cerebellum	SCAN
rs10843822	C12orf35	cis	parietal	SCAN
rs10843822	IPO8	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30849200-30881600	Weak transcription	Right Ventricle	heart
2	chr12:30849600-30881200	Weak transcription	Psoas Muscle	Psoas
3	chr12:30849600-30881600	Weak transcription	Aorta	Aorta
4	chr12:30857400-30881800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:30858000-30891800	Weak transcription	Fetal Heart	heart
6	chr12:30859200-30892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:30859400-30883400	Weak transcription	Colonic Mucosa	Colon
8	chr12:30860400-30881600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:30861400-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:30861400-30885000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
13	chr12:30861800-30884600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:30861800-30894600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:30861800-30895200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:30862200-30895000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:30862400-30895600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:30863400-30881600	Weak transcription	Gastric	stomach
19	chr12:30863400-30882800	Weak transcription	Brain Substantia Nigra	brain
20	chr12:30863400-30885200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:30863400-30891000	Weak transcription	GM12878-XiMat	blood
22	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
23	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:30864600-30905200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:30865000-30881600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:30865400-30881600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:30867200-30881600	Weak transcription	Lung	lung
28	chr12:30867400-30881600	Weak transcription	Esophagus	oesophagus
29	chr12:30867400-30884400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:30869600-30881600	Weak transcription	Brain Angular Gyrus	brain
31	chr12:30869600-30886000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:30869800-30889000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:30870600-30879200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:30871200-30881800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:30871400-30900800	Weak transcription	K562	blood
36	chr12:30871600-30881600	Weak transcription	Dnd41	blood
37	chr12:30871800-30881200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:30872200-30880600	Weak transcription	Brain Anterior Caudate	brain
39	chr12:30872200-30881600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:30872200-30881600	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:30872200-30886000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:30872200-30903800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:30872400-30879800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:30872400-30880400	Weak transcription	Fetal Kidney	kidney
45	chr12:30872400-30881200	Weak transcription	Brain Germinal Matrix	brain
46	chr12:30872400-30881600	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:30872400-30881600	Weak transcription	Thymus	Thymus
48	chr12:30872400-30903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:30873200-30880400	Strong transcription	Liver	Liver
50	chr12:30873200-30882400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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