Variant report

Variant	rs11189244
Chromosome Location	chr10:99267639-99267640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99261479..99263816-chr10:99267425..99269402,2	K562	blood:
2	chr10:99265449..99267822-chr10:99277534..99279101,2	K562	blood:
3	chr10:99266125..99268587-chr10:99272459..99275467,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10786351	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10882937	0.82[CHB][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap]
rs10882939	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs10882943	0.81[ASN][1000 genomes]
rs10882944	0.81[ASN][1000 genomes]
rs10882946	0.81[ASN][1000 genomes]
rs10882959	0.82[MEX][hapmap]
rs10882962	0.82[MEX][hapmap]
rs11189238	0.82[ASN][1000 genomes]
rs11189245	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11189249	0.85[LWK][hapmap];0.96[YRI][hapmap]
rs11189253	0.82[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11189259	0.82[MEX][hapmap]
rs11189275	0.88[MEX][hapmap]
rs11189281	0.82[CHB][hapmap]
rs12221474	0.82[MEX][hapmap]
rs12243136	0.82[CHB][hapmap]
rs12415482	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1572860	0.88[MEX][hapmap]
rs17112814	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2275583	0.82[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs4917772	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4919104	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs59109814	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7084687	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7089060	0.86[CHB][hapmap]
rs7096611	0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7893335	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7902642	0.82[MEX][hapmap]
rs7915501	0.92[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11189244	CCNJ	cis	cerebellum	SCAN
rs11189244	RRP12	cis	cerebellum	SCAN
rs11189244	KIAA0690	cis	multi-tissue	Pritchard
rs11189244	MMS19	cis	cerebellum	SCAN
rs11189244	RRP12	cis	parietal	SCAN
rs11189244	FAM178A	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99260200-99276800	Weak transcription	Pancreas	Pancrea
2	chr10:99260400-99269400	Weak transcription	Ovary	ovary
3	chr10:99260400-99271400	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:99260400-99272000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:99260600-99267800	Weak transcription	Osteobl	bone
6	chr10:99260600-99268000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:99260600-99268000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:99260600-99268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:99260600-99268200	Weak transcription	NH-A	brain
10	chr10:99260600-99270800	Weak transcription	Brain Angular Gyrus	brain
11	chr10:99260600-99271200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:99260800-99267800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:99260800-99267800	Weak transcription	HMEC	breast
14	chr10:99260800-99268000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:99260800-99268000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:99260800-99268000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:99260800-99270400	Weak transcription	Adipose Nuclei	Adipose
18	chr10:99260800-99276800	Weak transcription	HSMM	muscle
19	chr10:99261000-99267800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:99261000-99267800	Weak transcription	NHLF	lung
21	chr10:99261000-99270800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:99262000-99271600	Weak transcription	HepG2	liver
23	chr10:99262400-99267800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:99263400-99271600	Weak transcription	Lung	lung
25	chr10:99263600-99270800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:99263600-99277800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr10:99263800-99277200	Weak transcription	HSMMtube	muscle
28	chr10:99263800-99277600	Weak transcription	Aorta	Aorta
29	chr10:99264000-99271200	Weak transcription	Right Atrium	heart
30	chr10:99264000-99271600	Weak transcription	Fetal Muscle Leg	muscle
31	chr10:99264000-99271600	Weak transcription	Right Ventricle	heart
32	chr10:99264200-99267800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:99264200-99268000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:99264200-99271200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr10:99266200-99267800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr10:99266200-99270800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr10:99266200-99271200	Weak transcription	Left Ventricle	heart
38	chr10:99266200-99271800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr10:99266200-99272200	Weak transcription	Psoas Muscle	Psoas
40	chr10:99266200-99277600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr10:99266600-99277400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr10:99267000-99267800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr10:99267600-99267800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:99267600-99268400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr10:99267600-99268400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr10:99267600-99268400	Enhancers	Brain Cingulate Gyrus	brain
47	chr10:99267600-99268600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr10:99267600-99268600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:99267600-99268600	Enhancers	Brain Anterior Caudate	brain
50	chr10:99267600-99268800	Enhancers	HUES6 Cell Line	embryonic stem cell

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