Variant report

Variant	rs12448
Chromosome Location	chr11:10533952-10533953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:10532392-10535141	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10532333..10535020-chr11:10535560..10538529,2	K562	blood:
2	chr11:10533091..10536044-chr11:10536842..10539445,2	K562	blood:
3	chr11:10526046..10528232-chr11:10533609..10536011,2	K562	blood:

Variant related genes	Relation type
MTRNR2L8	TF binding region
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10458930	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10458931	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10500725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770124	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10840432	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840433	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840434	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840437	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042865	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042868	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042872	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042892	0.81[JPT][hapmap]
rs1350991	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1841811	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054391	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781862	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4146830	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910152	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7126551	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131588	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs728528	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7932321	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7939044	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs7943804	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs9300104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv972946	chr11:10523147-10534985	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1044011	chr11:10529353-10564450	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12448	AMPD3	cis	cerebellum	SCAN
rs12448	WEE1	cis	cerebellum	SCAN
rs12448	RNF141	cis	parietal	SCAN
rs12448	GALNTL4	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10501600-10550600	Weak transcription	Small Intestine	intestine
2	chr11:10502600-10560800	Weak transcription	Fetal Brain Male	brain
3	chr11:10507800-10544800	Weak transcription	Fetal Kidney	kidney
4	chr11:10512800-10540400	Weak transcription	Fetal Lung	lung
5	chr11:10512800-10548600	Weak transcription	Right Ventricle	heart
6	chr11:10513200-10538000	Weak transcription	Left Ventricle	heart
7	chr11:10513400-10536000	Weak transcription	A549	lung
8	chr11:10514600-10535600	Weak transcription	HSMM	muscle
9	chr11:10515800-10540600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:10516000-10544000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:10520000-10543400	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:10522200-10541200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:10522400-10535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:10522400-10537800	Weak transcription	Fetal Intestine Large	intestine
15	chr11:10522400-10540600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:10522400-10546200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:10522400-10560800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:10522800-10540600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:10524200-10537800	Weak transcription	Aorta	Aorta
20	chr11:10524600-10536800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:10524600-10540600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:10524600-10544800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:10525800-10555600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:10526200-10535400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:10526400-10536000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:10526400-10536200	Weak transcription	NHDF-Ad	bronchial
27	chr11:10526400-10537800	Weak transcription	Pancreas	Pancrea
28	chr11:10526400-10548800	Weak transcription	Spleen	Spleen
29	chr11:10526400-10549000	Weak transcription	Ovary	ovary
30	chr11:10526400-10551800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:10526400-10561600	Weak transcription	Colonic Mucosa	Colon
32	chr11:10526800-10537800	Weak transcription	Fetal Intestine Small	intestine
33	chr11:10526800-10548800	Weak transcription	Psoas Muscle	Psoas
34	chr11:10527000-10534200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr11:10527200-10537800	Weak transcription	Lung	lung
36	chr11:10527200-10540200	Weak transcription	Liver	Liver
37	chr11:10527200-10540200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:10527200-10540600	Weak transcription	Gastric	stomach
39	chr11:10527400-10534600	Strong transcription	Primary B cells from cord blood	blood
40	chr11:10527400-10535600	Weak transcription	NHLF	lung
41	chr11:10527600-10542400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:10527800-10535600	Weak transcription	Thymus	Thymus
43	chr11:10527800-10541000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:10528000-10540400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:10528000-10540600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr11:10528000-10540600	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:10528000-10542600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr11:10528200-10535600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr11:10528200-10536000	Weak transcription	Fetal Stomach	stomach
50	chr11:10528200-10536200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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