Variant report

Variant	rs10864898
Chromosome Location	chr2:112869041-112869042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112811397..112814372-chr2:112868078..112870931,3	K562	blood:

Variant related genes	Relation type
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10165845	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175143	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178449	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182333	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045300	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs10779884	0.97[ASN][1000 genomes]
rs12618637	0.90[ASN][1000 genomes]
rs28437819	0.82[AMR][1000 genomes]
rs4241121	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257409	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613287	0.85[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs4848993	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849007	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849044	0.90[ASN][1000 genomes]
rs6707397	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6730057	0.98[ASN][1000 genomes]
rs6731563	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737707	0.86[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs7577442	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580507	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581849	1.00[JPT][hapmap]
rs7591702	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595574	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308669	0.88[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653401	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653422	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10864898	POLR1B	cis	cerebellum	SCAN
rs10864898	FBLN7	cis	cerebellum	SCAN
rs10864898	POLR1B	cis	parietal	SCAN
rs10864898	CCDC138	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:112834600-112871200	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr2:112835800-112883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:112836000-112874400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:112843000-112869400	Weak transcription	Fetal Heart	heart
7	chr2:112845400-112875200	Weak transcription	Right Ventricle	heart
8	chr2:112851200-112881600	Weak transcription	Stomach Mucosa	stomach
9	chr2:112852000-112871200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:112853200-112871200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr2:112853200-112871200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:112853400-112871200	Strong transcription	Placenta	Placenta
13	chr2:112854400-112869400	Weak transcription	Esophagus	oesophagus
14	chr2:112855400-112871200	Strong transcription	NH-A	brain
15	chr2:112856800-112869400	Weak transcription	Aorta	Aorta
16	chr2:112856800-112869400	Weak transcription	Gastric	stomach
17	chr2:112856800-112869400	Weak transcription	Pancreas	Pancrea
18	chr2:112856800-112869400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:112856800-112869400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:112856800-112870200	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:112856800-112874200	Weak transcription	Lung	lung
22	chr2:112856800-112875600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:112856800-112881800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:112857000-112869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:112857000-112883000	Weak transcription	Hela-S3	cervix
26	chr2:112857000-112891200	Weak transcription	Small Intestine	intestine
27	chr2:112857200-112877600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:112857400-112869400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:112857400-112869400	Weak transcription	Spleen	Spleen
30	chr2:112859600-112877200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:112859800-112870600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:112860200-112871200	Strong transcription	Osteobl	bone
33	chr2:112863600-112870800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:112863800-112871200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:112864600-112871000	Strong transcription	HSMM	muscle
36	chr2:112864800-112869400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:112865200-112869600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:112865200-112870800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr2:112865400-112870400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:112865400-112871000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:112865400-112871200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:112865600-112869400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:112865800-112870400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:112866000-112870200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:112866200-112879000	Weak transcription	Psoas Muscle	Psoas
46	chr2:112866600-112869600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:112866600-112870400	ZNF genes & repeats	K562	blood
48	chr2:112866600-112871600	Weak transcription	Fetal Brain Male	brain
49	chr2:112866800-112869800	Weak transcription	Brain Anterior Caudate	brain
50	chr2:112866800-112871200	Strong transcription	Adipose Nuclei	Adipose

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