Variant report

Variant	rs539733599
Chromosome Location	chr1:226250018-226250019
allele	C/T
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	HDAC2	chr1:226249583-226250294	K562	blood:	n/a	n/a
2	POLR2A	chr1:226249047-226251609	Hela-S3	cervix:	n/a	n/a
3	CHD1	chr1:226248795-226252344	IMR90	lung:	n/a	chr1:226250205-226250215 chr1:226250686-226250696 chr1:226250156-226250166 chr1:226250759-226250769 chr1:226250029-226250039
4	POLR2A	chr1:226249356-226251735	GM18505	blood:	n/a	n/a
5	POLR2A	chr1:226249375-226251078	ECC-1	luminal epithelium:	n/a	n/a
6	CREB1	chr1:226249067-226250858	K562	blood:	n/a	n/a
7	MAX	chr1:226249418-226250589	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:226249449-226250625	A549	lung:	n/a	n/a
9	MXI1	chr1:226248834-226251514	Hela-S3	cervix:	n/a	n/a
10	TAF7	chr1:226249366-226252248	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr1:226249430-226250869	HepG2	liver:	n/a	n/a
12	YY1	chr1:226249133-226251486	SK-N-SH	brain:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
13	POLR2A	chr1:226249425-226250784	A549	lung:	n/a	n/a
14	POLR2A	chr1:226249360-226250644	HCT-116	colon:	n/a	n/a
15	JUND	chr1:226249500-226250779	A549	lung:	n/a	chr1:226250348-226250357
16	TEAD4	chr1:226249654-226250510	H1-hESC	embryonic stem cell:	n/a	n/a
17	CREB1	chr1:226249296-226250750	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:226249337-226251503	NB4	blood:	n/a	n/a
19	BCLAF1	chr1:226249142-226250288	K562	blood:	n/a	chr1:226249777-226249790 chr1:226249655-226249668 chr1:226249771-226249784 chr1:226249778-226249791 chr1:226250007-226250016
20	ESR1	chr1:226249535-226250092	ECC-1	luminal epithelium:	n/a	n/a
21	JUND	chr1:226249895-226250290	A549	lung:	n/a	n/a
22	MAX	chr1:226249409-226250502	K562	blood:	n/a	n/a
23	ETS1	chr1:226249986-226250750	A549	lung:	n/a	chr1:226250676-226250687
24	SIN3AK20	chr1:226249467-226251625	K562	blood:	n/a	n/a
25	PML	chr1:226249030-226251155	K562	blood:	n/a	n/a
26	ZBTB7A	chr1:226249543-226250308	K562	blood:	n/a	chr1:226249574-226249582
27	E2F6	chr1:226249594-226250589	K562	blood:	n/a	chr1:226249745-226249756 chr1:226249744-226249756 chr1:226249804-226249813 chr1:226250432-226250442 chr1:226250435-226250445 chr1:226250010-226250019 chr1:226250442-226250451 chr1:226250522-226250537
28	SP1	chr1:226249548-226250612	H1-hESC	embryonic stem cell:	n/a	chr1:226250029-226250038 chr1:226250119-226250130 chr1:226250035-226250049 chr1:226250028-226250042
29	EP300	chr1:226249968-226250251	H1-hESC	embryonic stem cell:	n/a	chr1:226250165-226250174
30	POLR2A	chr1:226249112-226251663	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr1:226249258-226251649	K562	blood:	n/a	chr1:226251147-226251156 chr1:226251147-226251156 chr1:226251146-226251157 chr1:226251148-226251155
32	POLR2A	chr1:226248810-226256763	K562	blood:	n/a	n/a
33	GABPA	chr1:226249397-226250887	K562	blood:	n/a	chr1:226249804-226249813 chr1:226250016-226250025 chr1:226249741-226249750 chr1:226250761-226250770
34	HEY1	chr1:226249385-226250754	HepG2	liver:	n/a	chr1:226250432-226250447 chr1:226250435-226250450
35	POLR2A	chr1:226249406-226250258	GM12878	blood:	n/a	n/a
36	HDAC2	chr1:226249970-226250197	H1-hESC	embryonic stem cell:	n/a	n/a
37	SMC3	chr1:226249106-226250838	Hela-S3	cervix:	n/a	chr1:226250669-226250683 chr1:226249498-226249505
38	YY1	chr1:226249298-226251372	HepG2	liver:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
39	ELF1	chr1:226249545-226250289	MCF-7	breast:	n/a	chr1:226250013-226250022
40	POLR2A	chr1:226249406-226250965	K562	blood:	n/a	n/a
41	E2F6	chr1:226249305-226250439	A549	lung:	n/a	chr1:226249745-226249756 chr1:226249744-226249756 chr1:226249804-226249813 chr1:226250010-226250019
42	POLR2A	chr1:226249126-226251671	K562	blood:	n/a	n/a
43	PBX3	chr1:226249517-226250670	SK-N-SH	brain:	n/a	n/a
44	REST	chr1:226249713-226250146	PANC-1	pancreas:	n/a	chr1:226249770-226249783 chr1:226250012-226250025
45	TCF7L2	chr1:226249398-226250952	HCT-116	colon:	n/a	n/a
46	YY1	chr1:226249326-226251539	GM12878	blood:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
47	FOXA1	chr1:226249718-226250403	HepG2	liver:	n/a	n/a
48	HEY1	chr1:226249983-226250264	HepG2	liver:	n/a	n/a
49	REST	chr1:226249585-226250196	HepG2	liver:	n/a	chr1:226249770-226249783 chr1:226250012-226250025
50	NFIC	chr1:226249490-226250143	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226249387..226250153-chr17:27046599..27047373,2	Hela-S3	cervix:
2	chr1:226053730..226055639-chr1:226248303..226251048,2	MCF-7	breast:
3	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
4	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
5	chr1:226249482..226250105-chr11:67777477..67778223,2	Hela-S3	cervix:
6	chr1:225964211..225968767-chr1:226248453..226252378,4	K562	blood:
7	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
8	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
9	chr1:226249145..226251355-chr5:138634621..138637026,2	MCF-7	breast:
10	chr1:226249721..226252045-chr1:226495735..226498532,3	K562	blood:
11	chr1:226249843..226250705-chr7:100026281..100026883,3	NB4	blood:
12	chr1:226249766..226250543-chr6:26216732..26217538,2	Hela-S3	cervix:
13	chr1:226249823..226250541-chr10:120937882..120938711,2	HCT-116	colon:
14	chr1:225614646..225616665-chr1:226249352..226251446,2	K562	blood:
15	chr1:225839962..225842492-chr1:226249684..226252539,2	MCF-7	breast:
16	chr1:45284133..45286762-chr1:226249402..226251655,2	K562	blood:
17	chr1:226249163..226250085-chr19:59010196..59010725,2	Hela-S3	cervix:
18	chr1:225838732..225840997-chr1:226248323..226251215,2	MCF-7	breast:
19	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
20	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
21	chr1:225964614..225966521-chr1:226248789..226250672,2	K562	blood:
22	chr1:226249432..226250174-chr19:50083021..50083902,2	Hela-S3	cervix:
23	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
24	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:

Variant related genes	Relation type
H3F3A	TF binding region
ENSG00000272562	TF binding region
ENSG00000154380	Chromatin interaction
ENSG00000165672	Chromatin interaction
ENSG00000198242	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000225518	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000199545	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000006534	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000183814	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000143815	Chromatin interaction
ENSG00000142546	Chromatin interaction
ENSG00000083807	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3327023	chr1:226248854-226251702	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a
4	esv3386707	chr1:226249329-226251427	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226248200-226253400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr1:226248800-226252600	Active TSS	NH-A	brain
3	chr1:226248800-226252800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:226248800-226252800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:226248800-226253000	Active TSS	NHLF	lung
6	chr1:226248800-226253200	Active TSS	Colonic Mucosa	Colon
7	chr1:226248800-226253400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:226248800-226253400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:226249000-226252400	Active TSS	HSMM	muscle
10	chr1:226249000-226252600	Active TSS	Colon Smooth Muscle	Colon
11	chr1:226249000-226252600	Active TSS	Fetal Brain Female	brain
12	chr1:226249000-226252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:226249000-226252800	Active TSS	Left Ventricle	heart
14	chr1:226249000-226253000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:226249000-226253000	Active TSS	Psoas Muscle	Psoas
16	chr1:226249000-226253200	Active TSS	Fetal Muscle Trunk	muscle
17	chr1:226249000-226253200	Active TSS	Ovary	ovary
18	chr1:226249000-226253400	Active TSS	Fetal Intestine Large	intestine
19	chr1:226249000-226253400	Active TSS	Right Ventricle	heart
20	chr1:226249200-226250600	Active TSS	HepG2	liver
21	chr1:226249200-226252000	Active TSS	Small Intestine	intestine
22	chr1:226249200-226252200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:226249200-226252200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:226249200-226252200	Active TSS	Esophagus	oesophagus
25	chr1:226249200-226252200	Active TSS	Lung	lung
26	chr1:226249200-226252200	Active TSS	Pancreas	Pancrea
27	chr1:226249200-226252400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:226249200-226252400	Active TSS	Brain Anterior Caudate	brain
29	chr1:226249200-226252400	Active TSS	Placenta Amnion	Placenta Amnion
30	chr1:226249200-226252600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:226249200-226252800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:226249200-226252800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:226249200-226252800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:226249200-226252800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:226249200-226252800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:226249200-226252800	Active TSS	Brain Germinal Matrix	brain
37	chr1:226249200-226253000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:226249200-226253000	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr1:226249200-226253000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:226249200-226253000	Active TSS	Aorta	Aorta
41	chr1:226249200-226253400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:226249200-226253400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:226249200-226253400	Active TSS	Fetal Intestine Small	intestine
44	chr1:226249400-226250600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:226249400-226250600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:226249400-226251400	Transcr. at gene 5' and 3'	Right Atrium	heart
47	chr1:226249400-226251800	Active TSS	Gastric	stomach
48	chr1:226249400-226252000	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:226249400-226252200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:226249400-226252200	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links