Variant report

Variant	rs142933780
Chromosome Location	chr1:10270161-10270162
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	SMARCB1	chr1:10269882-10271756	Hela-S3	cervix:	n/a	n/a
2	ZBTB7A	chr1:10270086-10270554	HepG2	liver:	n/a	chr1:10270410-10270419
3	POLR2A	chr1:10269907-10270194	A549	lung:	n/a	n/a
4	MTA3	chr1:10269780-10270767	GM12878	blood:	n/a	n/a
5	CTCF	chr1:10269726-10270767	A549	lung:	n/a	chr1:10270405-10270418 chr1:10270404-10270425 chr1:10270405-10270414 chr1:10270403-10270419 chr1:10270405-10270418 chr1:10270402-10270420 chr1:10269886-10269899 chr1:10270407-10270417
6	HDAC2	chr1:10269868-10270734	HepG2	liver:	n/a	chr1:10270654-10270663
7	CTCF	chr1:10270140-10270290	A549	lung:	n/a	n/a
8	POLR2A	chr1:10269845-10270997	Hela-S3	cervix:	n/a	n/a
9	MAX	chr1:10269851-10270729	A549	lung:	n/a	n/a
10	TBP	chr1:10269941-10270827	K562	blood:	n/a	n/a
11	TBL1XR1	chr1:10270084-10270651	GM12878	blood:	n/a	n/a
12	E2F6	chr1:10269986-10272096	K562	blood:	n/a	chr1:10271048-10271063 chr1:10271718-10271730 chr1:10270941-10270950 chr1:10270581-10270590 chr1:10271196-10271206 chr1:10270469-10270478
13	POLR2A	chr1:10269899-10270925	A549	lung:	n/a	n/a
14	POLR2A	chr1:10269845-10270848	HepG2	liver:	n/a	n/a
15	YY1	chr1:10270061-10270847	GM12878	blood:	n/a	chr1:10270821-10270835 chr1:10270827-10270841 chr1:10270800-10270811 chr1:10270691-10270705
16	CTCF	chr1:10269954-10270169	MCF-7	breast:	n/a	n/a
17	USF2	chr1:10270008-10270352	GM12878	blood:	n/a	n/a
18	YY1	chr1:10269913-10270688	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr1:10269861-10270563	Hela-S3	cervix:	n/a	chr1:10270300-10270310 chr1:10270404-10270418 chr1:10270430-10270443 chr1:10270408-10270418 chr1:10270403-10270422
20	POLR2A	chr1:10269683-10270824	U87	brain:	n/a	n/a
21	RAD21	chr1:10269870-10270733	MCF-7	breast:	n/a	chr1:10270300-10270310 chr1:10270404-10270418 chr1:10270430-10270443 chr1:10270408-10270418 chr1:10270403-10270422
22	SP4	chr1:10269926-10270690	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:10269865-10270798	K562	blood:	n/a	chr1:10270405-10270418 chr1:10270404-10270425 chr1:10270405-10270414 chr1:10270403-10270419 chr1:10270405-10270418 chr1:10270402-10270420 chr1:10269886-10269899 chr1:10270407-10270417
24	ATF2	chr1:10269759-10270603	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr1:10270142-10270644	K562	blood:	n/a	chr1:10270405-10270418 chr1:10270404-10270425 chr1:10270405-10270414 chr1:10270403-10270419 chr1:10270405-10270418 chr1:10270402-10270420 chr1:10270407-10270417
26	TBL1XR1	chr1:10270025-10270755	K562	blood:	n/a	n/a
27	CREB1	chr1:10270123-10270914	HepG2	liver:	n/a	n/a
28	NFYB	chr1:10269967-10270763	Hela-S3	cervix:	n/a	chr1:10270465-10270480 chr1:10270497-10270511 chr1:10270500-10270512 chr1:10270496-10270511 chr1:10270466-10270480 chr1:10270499-10270509 chr1:10270496-10270511 chr1:10270498-10270511 chr1:10270465-10270480
29	POLR2A	chr1:10269978-10270902	GM18951	blood:	n/a	n/a
30	CTCF	chr1:10269969-10270166	GM12892	blood:	n/a	n/a
31	CTCF	chr1:10269916-10270167	Gliobla	brain:	n/a	n/a
32	TBP	chr1:10269922-10270788	HepG2	liver:	n/a	n/a
33	FOXP2	chr1:10269985-10270253	SK-N-MC	brain:	n/a	n/a
34	RCOR1	chr1:10269781-10270807	Hela-S3	cervix:	n/a	n/a
35	GTF2F1	chr1:10269956-10270740	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr1:10270151-10270699	K562	blood:	n/a	chr1:10270405-10270418 chr1:10270404-10270425 chr1:10270405-10270414 chr1:10270403-10270419 chr1:10270405-10270418 chr1:10270402-10270420 chr1:10270407-10270417
37	PML	chr1:10269966-10270840	GM12878	blood:	n/a	chr1:10270017-10270025
38	TAF1	chr1:10269716-10271838	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF12	chr1:10269776-10270915	ECC-1	luminal epithelium:	n/a	chr1:10270427-10270437
40	POLR2A	chr1:10269999-10270898	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:10270140-10270940	GM12878	blood:	n/a	n/a
42	SP1	chr1:10270106-10270785	GM12878	blood:	n/a	chr1:10270570-10270579 chr1:10270489-10270510 chr1:10270240-10270249 chr1:10270240-10270254 chr1:10270239-10270251 chr1:10270241-10270250 chr1:10270240-10270249 chr1:10270239-10270251
43	ELF1	chr1:10269819-10271725	GM12878	blood:	n/a	chr1:10270352-10270364 chr1:10270829-10270841 chr1:10270994-10271003 chr1:10270828-10270840 chr1:10270747-10270759
44	CHD2	chr1:10269930-10270756	GM12878	blood:	n/a	n/a
45	TAF1	chr1:10269924-10270821	ECC-1	luminal epithelium:	n/a	n/a
46	ZNF143	chr1:10269961-10270650	Hela-S3	cervix:	n/a	chr1:10270525-10270535 chr1:10270580-10270590
47	HCFC1	chr1:10270062-10270847	K562	blood:	n/a	n/a
48	ARID3A	chr1:10269733-10270729	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr1:10270022-10270745	A549	lung:	n/a	n/a
50	CEBPB	chr1:10269906-10270653	Hela-S3	cervix:	n/a	chr1:10270469-10270477

No.	Distal block	Cell Line	Cell type
1	chr1:10269636..10272138-chr1:10457591..10460138,4	K562	blood:
2	chr1:10269968..10270783-chr1:86046649..86047447,2	Hela-S3	cervix:
3	chr1:10269768..10272241-chr11:62606834..62608360,2	MCF-7	breast:
4	chr1:10269869..10270448-chr12:64845349..64846337,2	Hela-S3	cervix:
5	chr1:10269993..10270712-chr1:10488254..10488767,2	K562	blood:
6	chr1:10269235..10270735-chr17:41462941..41466799,3	K562	blood:
7	chr1:10269508..10272201-chr1:10459062..10462119,3	K562	blood:

Variant related genes	Relation type
KIF1B	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000183735	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3440429	chr1:10269390-10271938	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	esv3406468	chr1:10269765-10272038	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	esv3406947	chr1:10269890-10272738	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10268600-10270400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:10269400-10270200	Flanking Active TSS	Dnd41	blood
3	chr1:10269400-10270800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:10269400-10271400	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:10269400-10272200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:10269400-10272400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:10269400-10272400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:10269400-10272400	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr1:10269400-10272400	Active TSS	NHDF-Ad	bronchial
10	chr1:10269400-10272600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:10269400-10272800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:10269400-10273200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:10269600-10270200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr1:10269600-10270200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr1:10269600-10270200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr1:10269600-10270200	Flanking Active TSS	NHEK	skin
17	chr1:10269600-10270400	Active TSS	Stomach Mucosa	stomach
18	chr1:10269600-10271200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:10269600-10271200	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:10269600-10271200	Active TSS	K562	blood
21	chr1:10269600-10271400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:10269600-10271800	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:10269600-10271800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:10269600-10271800	Active TSS	Primary T cells from cord blood	blood
25	chr1:10269600-10271800	Active TSS	Brain Hippocampus Middle	brain
26	chr1:10269600-10271800	Active TSS	Fetal Muscle Leg	muscle
27	chr1:10269600-10271800	Active TSS	Stomach Smooth Muscle	stomach
28	chr1:10269600-10272000	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:10269600-10272000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:10269600-10272000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:10269600-10272000	Active TSS	Fetal Stomach	stomach
32	chr1:10269600-10272200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr1:10269600-10272200	Active TSS	Brain Angular Gyrus	brain
34	chr1:10269600-10272400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr1:10269600-10272800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:10269600-10273200	Active TSS	HSMMtube	muscle
37	chr1:10269800-10270200	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr1:10269800-10270200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr1:10269800-10270200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:10269800-10270200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:10269800-10270200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:10269800-10270200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr1:10269800-10270200	Flanking Active TSS	Colonic Mucosa	Colon
44	chr1:10269800-10270200	Active TSS	Fetal Brain Male	brain
45	chr1:10269800-10270200	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr1:10269800-10270200	Active TSS	Right Atrium	heart
47	chr1:10269800-10270200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:10269800-10270200	Flanking Bivalent TSS/Enh	Thymus	Thymus
49	chr1:10269800-10270200	Flanking Active TSS	HMEC	breast
50	chr1:10269800-10270400	Flanking Active TSS	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links