Variant report

Variant	rs12126815
Chromosome Location	chr1:224401217-224401218
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	RCOR1	chr1:224401093-224402054	Hela-S3	cervix:	n/a	n/a
2	CEBPD	chr1:224401196-224401655	K562	blood:	n/a	n/a
3	TEAD4	chr1:224401139-224401858	K562	blood:	n/a	n/a
4	TBP	chr1:224400979-224401570	H1-hESC	embryonic stem cell:	n/a	n/a
5	SRF	chr1:224401200-224401377	GM12878	blood:	n/a	chr1:224401309-224401322 chr1:224401310-224401327 chr1:224401309-224401322 chr1:224401310-224401321 chr1:224401311-224401320 chr1:224401311-224401325 chr1:224401311-224401322
6	SRF	chr1:224401127-224401546	ECC-1	luminal epithelium:	n/a	chr1:224401309-224401322 chr1:224401310-224401327 chr1:224401309-224401322 chr1:224401310-224401321 chr1:224401311-224401320 chr1:224401311-224401325 chr1:224401311-224401322
7	CHD2	chr1:224401164-224401512	H1-hESC	embryonic stem cell:	n/a	n/a
8	SRF	chr1:224401043-224401515	H1-hESC	embryonic stem cell:	n/a	chr1:224401309-224401322 chr1:224401310-224401327 chr1:224401309-224401322 chr1:224401310-224401321 chr1:224401311-224401320 chr1:224401311-224401325 chr1:224401311-224401322
9	SMC3	chr1:224401215-224402178	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:224401142-224401668	H1-hESC	embryonic stem cell:	n/a	n/a
11	SRF	chr1:224400992-224401567	H1-hESC	embryonic stem cell:	n/a	chr1:224401309-224401322 chr1:224401310-224401327 chr1:224401309-224401322 chr1:224401310-224401321 chr1:224401311-224401320 chr1:224401311-224401325 chr1:224401311-224401322
12	RFX5	chr1:224401005-224402138	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:224401181-224401533	H1-hESC	embryonic stem cell:	n/a	n/a
14	RFX5	chr1:224401186-224401354	K562	blood:	n/a	n/a
15	TBP	chr1:224401214-224401965	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:224401166-224401754	Hela-S3	cervix:	n/a	n/a
17	BACH1	chr1:224401154-224401354	H1-hESC	embryonic stem cell:	n/a	n/a
18	TEAD4	chr1:224400992-224401485	ECC-1	luminal epithelium:	n/a	n/a
19	RFX5	chr1:224401161-224401469	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr1:224401038-224401460	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:224401131-224401873	H1-hESC	embryonic stem cell:	n/a	n/a
22	BRCA1	chr1:224401089-224402110	Hela-S3	cervix:	n/a	n/a
23	SP1	chr1:224400942-224401462	H1-hESC	embryonic stem cell:	n/a	n/a
24	TEAD4	chr1:224401002-224401489	H1-hESC	embryonic stem cell:	n/a	n/a
25	MXI1	chr1:224401194-224401638	Hela-S3	cervix:	n/a	n/a
26	JUND	chr1:224400964-224401585	H1-hESC	embryonic stem cell:	n/a	n/a
27	PRDM1	chr1:224401206-224401616	Hela-S3	cervix:	n/a	n/a
28	SRF	chr1:224401105-224401422	K562	blood:	n/a	chr1:224401309-224401322 chr1:224401310-224401327 chr1:224401309-224401322 chr1:224401310-224401321 chr1:224401311-224401320 chr1:224401311-224401325 chr1:224401311-224401322
29	SRF	chr1:224400993-224401659	ECC-1	luminal epithelium:	n/a	chr1:224401309-224401322 chr1:224401310-224401327 chr1:224401309-224401322 chr1:224401310-224401321 chr1:224401311-224401320 chr1:224401311-224401325 chr1:224401311-224401322

Variant related genes	Relation type
ENSG00000232628	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10799491	1.00[CEU][hapmap]
rs10799507	0.87[EUR][1000 genomes]
rs10799543	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10916458	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10916462	0.84[EUR][1000 genomes]
rs10916472	0.80[EUR][1000 genomes]
rs10916497	0.84[EUR][1000 genomes]
rs10916498	0.81[EUR][1000 genomes]
rs12082619	0.84[EUR][1000 genomes]
rs12083770	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12117480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12120308	0.80[EUR][1000 genomes]
rs12124547	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12126765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12128376	1.00[AFR][1000 genomes]
rs12133599	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12140137	0.84[EUR][1000 genomes]
rs12184283	0.84[EUR][1000 genomes]
rs45583539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56105022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.80[EUR][1000 genomes]
rs6686449	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6694451	1.00[CEU][hapmap]
rs68073536	0.81[EUR][1000 genomes]
rs72751651	1.00[AFR][1000 genomes]
rs72753956	0.87[EUR][1000 genomes]
rs72753969	0.87[EUR][1000 genomes]
rs72753994	0.80[EUR][1000 genomes]
rs72754000	0.84[EUR][1000 genomes]
rs72755905	0.84[EUR][1000 genomes]
rs7514140	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7552239	0.84[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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
5	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:224394000-224414600	Weak transcription	HMEC	breast
7	chr1:224396800-224402200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:224397000-224401800	Enhancers	Fetal Muscle Leg	muscle
9	chr1:224397600-224402200	Enhancers	Fetal Intestine Small	intestine
10	chr1:224397600-224402400	Enhancers	Stomach Mucosa	stomach
11	chr1:224397800-224402400	Enhancers	HepG2	liver
12	chr1:224398000-224401600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:224398000-224402400	Enhancers	Fetal Intestine Large	intestine
14	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
15	chr1:224398400-224401400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:224398600-224401800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:224398800-224401400	Enhancers	Hela-S3	cervix
18	chr1:224398800-224401800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:224399000-224402200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:224399200-224402200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:224399400-224401400	Weak transcription	Left Ventricle	heart
22	chr1:224399400-224403600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:224399400-224406600	Weak transcription	Pancreas	Pancrea
24	chr1:224399400-224411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
26	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:224399600-224401400	Weak transcription	Fetal Kidney	kidney
28	chr1:224399600-224401800	Enhancers	A549	lung
29	chr1:224399600-224405600	Weak transcription	Fetal Lung	lung
30	chr1:224400000-224401400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:224400000-224402000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:224400200-224401400	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:224400200-224401400	Enhancers	Right Ventricle	heart
34	chr1:224400200-224401600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:224400200-224401800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:224400200-224401800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr1:224400200-224401800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:224400200-224401800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr1:224400200-224401800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:224400200-224401800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:224400200-224401800	Enhancers	Placenta	Placenta
42	chr1:224400200-224401800	Enhancers	Small Intestine	intestine
43	chr1:224400200-224402200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:224400200-224402200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:224400200-224402200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:224400400-224401800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr1:224400400-224401800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr1:224400400-224401800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:224400400-224402200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:224400600-224401600	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links