Variant report

Variant	rs9925553
Chromosome Location	chr1:101411908-101411909
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	SPI1	chr1:101411727-101411924	K562	blood:	n/a	n/a
2	SPI1	chr1:101411535-101411956	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
HNRNPA1P68	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11647392	0.81[ASN][1000 genomes]
rs12019043	0.89[AMR][1000 genomes]
rs12921820	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2217271	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2217272	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2903042	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35456341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36003824	0.88[EUR][1000 genomes]
rs36053312	0.81[ASN][1000 genomes]
rs3919630	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4381587	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62027316	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62027318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6498334	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68129625	0.98[AFR][1000 genomes]
rs7194367	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7197089	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7200211	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7206775	0.89[AMR][1000 genomes]
rs8056508	0.83[ASN][1000 genomes]
rs8058440	0.82[ASN][1000 genomes]
rs8062074	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8063664	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8063669	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9673274	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9673275	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9673279	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806831	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806858	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9806943	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9925372	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9927247	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9927256	0.90[EUR][1000 genomes]
rs9927760	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9930701	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9936549	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9937086	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9938852	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9939998	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522064	chr1:101181342-101539866	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1012496	chr1:101295719-101466511	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535033	chr1:101295719-101466511	Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1001142	chr1:101399403-101783520	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535034	chr1:101399403-101783520	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv946098	chr1:101403971-101415950	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:101362400-101414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:101362600-101414800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:101362600-101414800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:101363000-101489600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:101363200-101416400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:101372200-101414800	Weak transcription	Esophagus	oesophagus
7	chr1:101378200-101414600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:101379400-101416400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:101379800-101414600	Weak transcription	Colonic Mucosa	Colon
10	chr1:101381600-101428800	Weak transcription	Fetal Brain Female	brain
11	chr1:101381600-101431200	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:101382400-101431600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:101383000-101434200	Weak transcription	Fetal Brain Male	brain
14	chr1:101383200-101414800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:101385000-101414200	Weak transcription	Stomach Mucosa	stomach
16	chr1:101389600-101418000	Weak transcription	HMEC	breast
17	chr1:101392000-101414600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:101392000-101416400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:101392200-101431200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:101392600-101414600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:101392600-101463800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:101393200-101415400	Weak transcription	NHLF	lung
23	chr1:101393200-101430000	Weak transcription	Hela-S3	cervix
24	chr1:101394000-101420000	Weak transcription	NHDF-Ad	bronchial
25	chr1:101398400-101421200	Weak transcription	NH-A	brain
26	chr1:101401000-101416200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:101401400-101416000	Weak transcription	Fetal Heart	heart
28	chr1:101403600-101414800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:101404400-101414800	Weak transcription	K562	blood
30	chr1:101404600-101471400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:101404800-101415200	Weak transcription	Psoas Muscle	Psoas
32	chr1:101404800-101435200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:101406800-101431400	Weak transcription	Brain Germinal Matrix	brain
34	chr1:101407000-101415200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:101407200-101416200	Weak transcription	HSMMtube	muscle
36	chr1:101407400-101417000	Weak transcription	Fetal Intestine Large	intestine
37	chr1:101407400-101468200	Weak transcription	Right Ventricle	heart
38	chr1:101407600-101414800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:101407600-101414800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:101407600-101414800	Weak transcription	Gastric	stomach
41	chr1:101407600-101414800	Weak transcription	Lung	lung
42	chr1:101407600-101414800	Weak transcription	Pancreas	Pancrea
43	chr1:101407600-101414800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:101407600-101414800	Weak transcription	NHEK	skin
45	chr1:101407600-101415000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:101407600-101416200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:101407600-101417000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:101407600-101430000	Weak transcription	Ovary	ovary
49	chr1:101407600-101448200	Weak transcription	Aorta	Aorta
50	chr1:101407800-101415200	Weak transcription	Stomach Smooth Muscle	stomach

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