Variant report

Variant	rs10915932
Chromosome Location	chr1:226271290-226271291
allele	A/C
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	PML	chr1:226271003-226271630	MCF-7	breast:	n/a	n/a
2	ZBTB7A	chr1:226271171-226271508	K562	blood:	n/a	n/a
3	UBTF	chr1:226270692-226271519	K562	blood:	n/a	n/a
4	EGR1	chr1:226271047-226271478	K562	blood:	n/a	chr1:226271254-226271268 chr1:226271385-226271395 chr1:226271285-226271299 chr1:226271288-226271298 chr1:226271288-226271301
5	MAX	chr1:226270487-226271728	HUVEC	blood vessel:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
6	HCFC1	chr1:226270389-226271769	Hela-S3	cervix:	n/a	n/a
7	ELK1	chr1:226271058-226271403	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:226270978-226271912	MCF10A-Er-Src	breast:	n/a	n/a
9	MXI1	chr1:226270714-226271767	HepG2	liver:	n/a	n/a
10	E2F6	chr1:226270627-226271648	K562	blood:	n/a	chr1:226271513-226271523 chr1:226271481-226271493
11	MXI1	chr1:226271067-226271331	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:226271001-226271511	HepG2	liver:	n/a	n/a
13	SMARCB1	chr1:226270565-226271883	Hela-S3	cervix:	n/a	n/a
14	CBX3	chr1:226271038-226271311	K562	blood:	n/a	n/a
15	ELF1	chr1:226271055-226271429	K562	blood:	n/a	n/a
16	TAF1	chr1:226271077-226271385	K562	blood:	n/a	n/a
17	USF1	chr1:226270915-226271674	H1-hESC	embryonic stem cell:	n/a	chr1:226271222-226271243 chr1:226271228-226271237 chr1:226271226-226271239 chr1:226271555-226271571 chr1:226271227-226271236 chr1:226271228-226271237 chr1:226271227-226271238 chr1:226271229-226271238
18	RUNX3	chr1:226271043-226271500	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:226271085-226271526	A549	lung:	n/a	n/a
20	POLR2A	chr1:226270967-226271360	GM12892	blood:	n/a	n/a
21	SIN3AK20	chr1:226270677-226271611	SK-N-SH	brain:	n/a	n/a
22	MAX	chr1:226270531-226271932	MCF-7	breast:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
23	POLR2A	chr1:226270794-226271518	GM19193	blood:	n/a	n/a
24	BHLHE40	chr1:226271026-226271375	GM12878	blood:	n/a	chr1:226271222-226271243 chr1:226271228-226271237 chr1:226271226-226271239 chr1:226271227-226271236 chr1:226271228-226271237 chr1:226271229-226271238
25	ZC3H11A	chr1:226271047-226271593	K562	blood:	n/a	n/a
26	POLR2A	chr1:226271061-226271307	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr1:226270454-226271734	K562	blood:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
28	THAP1	chr1:226270675-226271598	K562	blood:	n/a	n/a
29	POLR2A	chr1:226271024-226271496	H1-neurons	neurons:	n/a	n/a
30	MAX	chr1:226270511-226271939	A549	lung:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
31	POLR2A	chr1:226270911-226271638	GM18951	blood:	n/a	n/a
32	TAF1	chr1:226270960-226271474	PFSK-1	brain:	n/a	n/a
33	CHD2	chr1:226270816-226271507	GM12878	blood:	n/a	chr1:226270981-226270991 chr1:226270988-226270998
34	EP300	chr1:226271184-226271354	K562	blood:	n/a	n/a
35	CBX3	chr1:226270300-226271707	K562	blood:	n/a	n/a
36	MXI1	chr1:226270157-226272016	SK-N-SH	brain:	n/a	n/a
37	MAX	chr1:226270650-226271700	A549	lung:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
38	MAX	chr1:226270430-226271996	HCT-116	colon:	n/a	chr1:226270983-226270993 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226271228-226271237 chr1:226270877-226270886 chr1:226271292-226271301
39	MXI1	chr1:226271033-226271515	GM12878	blood:	n/a	n/a
40	USF1	chr1:226270886-226271507	A549	lung:	n/a	chr1:226271222-226271243 chr1:226271228-226271237 chr1:226271226-226271239 chr1:226271227-226271236 chr1:226271228-226271237 chr1:226271227-226271238 chr1:226271229-226271238
41	FOS	chr1:226271111-226271338	MCF10A-Er-Src	breast:	n/a	n/a
42	USF1	chr1:226270556-226271867	SK-N-SH	brain:	n/a	chr1:226271222-226271243 chr1:226271228-226271237 chr1:226271226-226271239 chr1:226271555-226271571 chr1:226271227-226271236 chr1:226271228-226271237 chr1:226271227-226271238 chr1:226271229-226271238
43	RCOR1	chr1:226271027-226271742	HepG2	liver:	n/a	n/a
44	CTCF	chr1:226271220-226271370	GM12867	blood:	n/a	chr1:226271289-226271302
45	ZNF143	chr1:226271104-226271335	K562	blood:	n/a	n/a
46	GTF2F1	chr1:226271076-226271531	K562	blood:	n/a	n/a
47	POLR2A	chr1:226271027-226271485	GM12878	blood:	n/a	n/a
48	SMC3	chr1:226271182-226271365	K562	blood:	n/a	n/a
49	POLR2A	chr1:226270684-226271507	GM12892	blood:	n/a	n/a
50	POLR2A	chr1:226270599-226271460	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226184976..226187995-chr1:226271007..226274594,3	K562	blood:
2	chr1:226271235..226271796-chrX:15692885..15693487,2	Hela-S3	cervix:
3	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
4	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
5	chr1:226270770..226272699-chr1:226374583..226377096,2	MCF-7	breast:
6	chr1:226185497..226187877-chr1:226269946..226272750,2	MCF-7	breast:
7	chr1:226270697..226271458-chr19:17402924..17403905,2	Hela-S3	cervix:
8	chr1:226250063..226250819-chr1:226271085..226271750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225518	TF binding region
ENSG00000186312	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000130312	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000223570	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10799335	0.87[EUR][1000 genomes]
rs10915927	0.80[AFR][1000 genomes]
rs10915930	0.92[EUR][1000 genomes]
rs10915931	0.92[EUR][1000 genomes]
rs12060155	0.95[EUR][1000 genomes]
rs12066979	0.94[EUR][1000 genomes]
rs12086044	0.87[EUR][1000 genomes]
rs12096468	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12096737	0.96[EUR][1000 genomes]
rs12117683	0.84[AFR][1000 genomes]
rs1877158	0.81[AFR][1000 genomes]
rs3768543	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4271181	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426098	0.81[AFR][1000 genomes]
rs6678547	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6679192	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6681021	0.92[EUR][1000 genomes]
rs6692329	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6692849	0.95[EUR][1000 genomes]
rs6700189	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7543135	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10915932	H3F3A	cis	Thyroid	GTEx
rs10915932	H3F3A	cis	Muscle Skeletal	GTEx
rs10915932	H3F3A	cis	Whole Blood	GTEx
rs10915932	H3F3A	cis	Esophagus Mucosa	GTEx
rs10915932	H3F3A	cis	Artery Tibial	GTEx
rs10915932	H3F3A	cis	Adipose Subcutaneous	GTEx
rs10915932	H3F3A	cis	Nerve Tibial	GTEx
rs10915932	H3F3A	cis	Esophagus Muscularis	GTEx
rs10915932	H3F3A	cis	Artery Aorta	GTEx
rs10915932	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226270200-226271400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr1:226270400-226271400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:226270400-226271800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:226270400-226271800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr1:226270400-226271800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr1:226270400-226271800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:226270400-226271800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:226270400-226271800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:226270400-226271800	Flanking Active TSS	Liver	Liver
10	chr1:226270400-226271800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:226270400-226271800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr1:226270400-226271800	Flanking Active TSS	Dnd41	blood
13	chr1:226270400-226272000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:226270400-226272000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:226270400-226272000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:226270400-226272000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr1:226270400-226272000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr1:226270400-226272000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:226270400-226272000	Flanking Active TSS	Colonic Mucosa	Colon
20	chr1:226270400-226272000	Active TSS	Rectal Smooth Muscle	rectum
21	chr1:226270600-226271600	Active TSS	Colon Smooth Muscle	Colon
22	chr1:226270600-226271600	Weak transcription	Fetal Heart	heart
23	chr1:226270600-226271600	Active TSS	Small Intestine	intestine
24	chr1:226270600-226271600	Flanking Active TSS	HMEC	breast
25	chr1:226270600-226271800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr1:226270600-226271800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:226270600-226271800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:226270600-226271800	Active TSS	Aorta	Aorta
29	chr1:226270600-226271800	Active TSS	Fetal Kidney	kidney
30	chr1:226270600-226271800	Active TSS	Right Atrium	heart
31	chr1:226270600-226271800	Active TSS	HSMMtube	muscle
32	chr1:226270600-226271800	Active TSS	NHDF-Ad	bronchial
33	chr1:226270600-226272000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:226270600-226272000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:226270600-226272000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:226270600-226272000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:226270600-226272000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:226270600-226272000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:226270600-226272000	Active TSS	Brain Angular Gyrus	brain
40	chr1:226270600-226272000	Active TSS	Brain Cingulate Gyrus	brain
41	chr1:226270600-226272000	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr1:226270600-226272000	Enhancers	Fetal Brain Male	brain
43	chr1:226270600-226272000	Active TSS	Psoas Muscle	Psoas
44	chr1:226270600-226272000	Active TSS	Hela-S3	cervix
45	chr1:226270800-226271400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:226270800-226271400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:226270800-226271400	Active TSS	Gastric	stomach
48	chr1:226270800-226271400	Active TSS	GM12878-XiMat	blood
49	chr1:226270800-226271400	Bivalent/Poised TSS	HepG2	liver
50	chr1:226270800-226271600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links