Variant report

Variant	rs58847346
Chromosome Location	chr10:23004262-23004263
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	chr10:23001941-23004344	GM12892	blood:	n/a	n/a
2	JUND	chr10:23004248-23004363	K562	blood:	n/a	n/a
3	MAZ	chr10:23001569-23004394	IMR90	lung:	n/a	n/a
4	POLR2A	chr10:23001201-23004277	GM18505	blood:	n/a	n/a
5	POLR2A	chr10:23001832-23004525	GM12892	blood:	n/a	n/a
6	BHLHE40	chr10:23002959-23004372	K562	blood:	n/a	chr10:23003671-23003687 chr10:23003674-23003690 chr10:23003663-23003679 chr10:23003492-23003508 chr10:23003020-23003036
7	POLR2A	chr10:23001700-23004437	GM19099	blood:	n/a	n/a
8	POLR2A	chr10:23002749-23004389	GM12892	blood:	n/a	n/a
9	POLR2A	chr10:23001985-23004290	K562	blood:	n/a	n/a
10	GTF2F1	chr10:23004237-23004317	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAZ	chr10:23001690-23004494	K562	blood:	n/a	n/a
12	POLR2A	chr10:23001999-23004410	Raji	blood:	n/a	n/a
13	STAT1	chr10:23004219-23004364	GM12878	blood:	n/a	n/a
14	MAX	chr10:23002092-23004350	A549	lung:	n/a	n/a
15	POLR2A	chr10:23001241-23004415	GM12878	blood:	n/a	n/a
16	POLR2A	chr10:23002823-23004264	K562	blood:	n/a	n/a
17	ZNF384	chr10:23004004-23004421	K562	blood:	n/a	n/a
18	POLR2A	chr10:23001975-23004321	GM18951	blood:	n/a	n/a
19	POLR2A	chr10:22999999-23004481	PBDE	blood:	n/a	n/a
20	TBL1XR1	chr10:23003819-23004396	K562	blood:	n/a	n/a
21	POLR2A	chr10:23002893-23004514	GM12891	blood:	n/a	n/a
22	POLR2A	chr10:23001556-23004555	GM12878	blood:	n/a	n/a
23	MTA3	chr10:23003619-23004509	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:23002012-23004359	K562	blood:	n/a	n/a
25	POLR2A	chr10:23002249-23004340	GM18526	blood:	n/a	n/a
26	POLR2A	chr10:23003559-23004360	K562	blood:	n/a	n/a
27	HCFC1	chr10:23003098-23004436	K562	blood:	n/a	n/a
28	RAD21	chr10:23002911-23004369	IMR90	lung:	n/a	chr10:23003842-23003855 chr10:23002944-23002954 chr10:23002937-23002949

No.	Distal block	Cell Line	Cell type
1	chr10:22862798..22864758-chr10:23003498..23006178,2	K562	blood:
2	chr10:23004207..23005718-chr10:23006215..23007803,2	K562	blood:
3	chr10:23003493..23005808-chr10:23014761..23017222,2	MCF-7	breast:
4	chr10:22606981..22611063-chr10:23000780..23004970,4	K562	blood:

Variant related genes	Relation type
PIP4K2A	TF binding region
ENSG00000269897	Chromatin interaction
ENSG00000168283	Chromatin interaction
ENSG00000148444	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1343505	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1544228	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16922558	0.84[ASN][1000 genomes]
rs16922574	0.84[ASN][1000 genomes]
rs16922619	0.95[ASN][1000 genomes]
rs16922627	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16922629	0.95[ASN][1000 genomes]
rs16922631	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16922641	0.91[ASN][1000 genomes]
rs16922673	0.88[ASN][1000 genomes]
rs16922694	0.81[EUR][1000 genomes]
rs2068726	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2153534	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55855627	0.88[ASN][1000 genomes]
rs56310787	0.81[EUR][1000 genomes]
rs56412842	0.84[ASN][1000 genomes]
rs57280862	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58587913	0.91[ASN][1000 genomes]
rs59134467	0.88[ASN][1000 genomes]
rs59278361	0.88[ASN][1000 genomes]
rs59573145	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59908513	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60284138	0.84[ASN][1000 genomes]
rs61295423	0.88[ASN][1000 genomes]
rs61587496	0.88[ASN][1000 genomes]
rs6482231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6482237	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67864649	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7070712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7078244	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72816902	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73598599	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73598600	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73598601	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73600503	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs74121608	0.86[ASN][1000 genomes]
rs74121889	0.95[ASN][1000 genomes]
rs74121891	0.95[ASN][1000 genomes]
rs74121893	0.95[ASN][1000 genomes]
rs74121894	0.95[ASN][1000 genomes]
rs74121897	0.95[ASN][1000 genomes]
rs74125205	0.95[ASN][1000 genomes]
rs74125206	0.95[ASN][1000 genomes]
rs7906229	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7914338	0.82[ASN][1000 genomes]
rs7917205	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9651370	0.81[EUR][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	esv1830947	chr10:22881196-23004381	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv831809	chr10:22918101-23069676	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3330079	chr10:23002696-23004844	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23001000-23004400	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:23001400-23004400	Active TSS	HSMMtube	muscle
3	chr10:23002000-23004400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:23002000-23004600	Active TSS	Colon Smooth Muscle	Colon
5	chr10:23003600-23004400	Flanking Active TSS	Dnd41	blood
6	chr10:23003600-23004400	Flanking Active TSS	HMEC	breast
7	chr10:23003800-23004400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr10:23003800-23004400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:23003800-23004400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr10:23003800-23004400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr10:23003800-23004400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:23003800-23004400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr10:23003800-23004400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:23003800-23004400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr10:23003800-23004400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr10:23003800-23004400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr10:23003800-23004400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr10:23003800-23004400	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr10:23003800-23004400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr10:23003800-23004400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:23003800-23004400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr10:23003800-23004400	Enhancers	Fetal Heart	heart
23	chr10:23003800-23004400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr10:23003800-23004400	Flanking Active TSS	GM12878-XiMat	blood
25	chr10:23003800-23004400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr10:23004000-23004400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr10:23004000-23004400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:23004000-23004400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:23004000-23004400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr10:23004000-23004400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr10:23004000-23004400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:23004000-23004400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr10:23004000-23004400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:23004000-23004400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr10:23004000-23004400	Enhancers	Esophagus	oesophagus
36	chr10:23004000-23004400	Enhancers	Gastric	stomach
37	chr10:23004000-23004400	Flanking Active TSS	Lung	lung
38	chr10:23004000-23004400	Enhancers	Spleen	Spleen
39	chr10:23004200-23004400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
40	chr10:23004200-23004400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:23004200-23004400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:23004200-23004400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr10:23004200-23004400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr10:23004200-23004400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
45	chr10:23004200-23004400	Enhancers	Primary T cells from cord blood	blood
46	chr10:23004200-23004400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr10:23004200-23004400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr10:23004200-23004400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:23004200-23004400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr10:23004200-23004400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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