Variant report

Variant	rs3811541
Chromosome Location	chr2:127413135-127413136
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	RCOR1	chr2:127412474-127413615	K562	blood:	n/a	n/a
2	TBL1XR1	chr2:127412785-127414219	K562	blood:	n/a	n/a
3	NFATC1	chr2:127413037-127413572	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:127413132-127414068	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:127412552-127417536	K562	blood:	n/a	n/a
6	POLR2A	chr2:127413116-127416167	GM12892	blood:	n/a	n/a
7	MAX	chr2:127412432-127414432	K562	blood:	n/a	n/a
8	RELA	chr2:127412736-127416116	GM12891	blood:	n/a	n/a
9	EP300	chr2:127412607-127413838	K562	blood:	n/a	chr2:127413334-127413350 chr2:127412920-127412930
10	CBX3	chr2:127412716-127413774	K562	blood:	n/a	n/a
11	WRNIP1	chr2:127413105-127413380	GM12878	blood:	n/a	n/a
12	MAFK	chr2:127413009-127413692	K562	blood:	n/a	n/a
13	MXI1	chr2:127413015-127416109	GM12878	blood:	n/a	n/a
14	RELA	chr2:127412920-127413927	GM18505	blood:	n/a	n/a
15	ZNF384	chr2:127412598-127414279	K562	blood:	n/a	n/a
16	MYC	chr2:127412553-127416132	K562	blood:	n/a	chr2:127414864-127414873 chr2:127414671-127414680 chr2:127415837-127415846 chr2:127414843-127414853
17	POLR2A	chr2:127412455-127417302	IMR90	lung:	n/a	n/a
18	EP300	chr2:127413007-127413754	GM12878	blood:	n/a	chr2:127413334-127413350
19	TEAD4	chr2:127412425-127413992	K562	blood:	n/a	n/a
20	POLR2A	chr2:127412576-127416145	K562	blood:	n/a	n/a
21	IRF1	chr2:127412725-127413858	K562	blood:	n/a	chr2:127413516-127413530 chr2:127413519-127413536 chr2:127413518-127413532 chr2:127413512-127413532 chr2:127413520-127413530
22	RELA	chr2:127413095-127413933	GM19099	blood:	n/a	n/a
23	JUN	chr2:127412363-127417264	K562	blood:	n/a	chr2:127417211-127417222
24	RELA	chr2:127413092-127413941	GM18951	blood:	n/a	n/a
25	RUNX3	chr2:127413133-127414005	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:127412576-127420620	PBDE	blood:	n/a	n/a
27	UBTF	chr2:127412613-127416015	K562	blood:	n/a	n/a
28	BHLHE40	chr2:127412638-127416254	K562	blood:	n/a	chr2:127413932-127413948 chr2:127413940-127413956
29	MYC	chr2:127412453-127415923	K562	blood:	n/a	chr2:127414864-127414873 chr2:127414671-127414680 chr2:127415837-127415846 chr2:127414843-127414853
30	POLR2A	chr2:127412810-127417778	GM12891	blood:	n/a	n/a
31	POLR2A	chr2:127413120-127416171	HL-60	blood:	n/a	n/a
32	MAX	chr2:127413105-127416148	NB4	blood:	n/a	chr2:127414864-127414873 chr2:127414671-127414680 chr2:127415837-127415846 chr2:127414843-127414853
33	RELA	chr2:127413082-127416141	GM15510	blood:	n/a	n/a
34	POLR2A	chr2:127412624-127416164	K562	blood:	n/a	n/a
35	RCOR1	chr2:127412678-127416249	IMR90	lung:	n/a	n/a
36	RCOR1	chr2:127412442-127414343	K562	blood:	n/a	n/a
37	MAX	chr2:127412559-127414357	K562	blood:	n/a	n/a
38	GATA1	chr2:127412594-127415107	PBDE	blood:	n/a	n/a
39	RELA	chr2:127413033-127413938	GM12892	blood:	n/a	n/a
40	MTA3	chr2:127413087-127416294	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
GYPC	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10928978	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10928979	0.92[ASN][1000 genomes]
rs12468467	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13008888	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13395010	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.99[ASN][1000 genomes]
rs1550407	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1813402	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960696	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099732	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099733	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119151	0.99[ASN][1000 genomes]
rs2119152	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2165226	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404961	0.97[ASN][1000 genomes]
rs28387094	0.96[ASN][1000 genomes]
rs28387096	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6431169	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002265	chr2:127029745-127733458	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535919	chr2:127029745-127733458	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583011	chr2:127386211-127489031	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875000	chr2:127402833-127423066	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875001	chr2:127402833-127431312	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong 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 lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv875002	chr2:127412013-127420211	Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv875003	chr2:127412495-127419582	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv875004	chr2:127412495-127420211	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3811541	BARHL2	trans	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127410800-127414200	Weak transcription	Hela-S3	cervix
2	chr2:127412400-127413200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:127412400-127413200	Enhancers	Fetal Thymus	thymus
4	chr2:127412400-127413600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:127412600-127413200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr2:127412600-127413200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:127412600-127413200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:127412600-127413200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr2:127412600-127413200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:127412600-127413200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:127412600-127413200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:127412600-127413200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:127412600-127413200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:127412600-127413200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:127412600-127413200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:127412600-127413200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:127412600-127413200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr2:127412600-127413200	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr2:127412600-127413200	Enhancers	Placenta	Placenta
20	chr2:127412600-127413200	Enhancers	Psoas Muscle	Psoas
21	chr2:127412600-127413200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr2:127412600-127413200	Enhancers	Right Atrium	heart
23	chr2:127412600-127413200	Enhancers	Right Ventricle	heart
24	chr2:127412600-127413200	Enhancers	Spleen	Spleen
25	chr2:127412600-127413400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:127412600-127413400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:127412600-127413400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr2:127412600-127413400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr2:127412600-127413400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr2:127412600-127413400	Flanking Active TSS	K562	blood
31	chr2:127412600-127413600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:127412600-127413600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr2:127412800-127413200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr2:127412800-127413200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:127412800-127413200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:127412800-127413200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:127412800-127413200	Enhancers	Liver	Liver
38	chr2:127412800-127413200	Enhancers	Brain Angular Gyrus	brain
39	chr2:127412800-127413200	Enhancers	Brain Anterior Caudate	brain
40	chr2:127412800-127413200	Enhancers	Brain Hippocampus Middle	brain
41	chr2:127412800-127413200	Enhancers	Brain Substantia Nigra	brain
42	chr2:127412800-127413200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr2:127412800-127413200	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr2:127412800-127413200	Enhancers	Ovary	ovary
45	chr2:127412800-127413200	Enhancers	Pancreas	Pancrea
46	chr2:127412800-127413200	Enhancers	HSMMtube	muscle
47	chr2:127412800-127413400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:127412800-127413400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:127412800-127413400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr2:127412800-127413400	Flanking Active TSS	Colon Smooth Muscle	Colon

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