Variant report

Variant	rs10164457
Chromosome Location	chr2:142889137-142889138
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	REST	chr2:142887426-142889581	H1-neurons	neurons:	n/a	chr2:142888105-142888115
2	CHD1	chr2:142888716-142889277	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:142888900-142889400	PFSK-1	brain:	n/a	n/a
4	RFX5	chr2:142888979-142889186	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:142888035-142889284	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr2:142889001-142889287	HepG2	liver:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
7	SMC3	chr2:142887840-142889409	Hela-S3	cervix:	n/a	n/a
8	SMARCC2	chr2:142887473-142889383	Hela-S3	cervix:	n/a	chr2:142889119-142889128
9	POLR2A	chr2:142887897-142889482	Hela-S3	cervix:	n/a	n/a
10	CHD2	chr2:142888955-142889158	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr2:142889016-142889319	K562	blood:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
12	POLR2A	chr2:142887853-142889198	HEK293	kidney:	n/a	n/a
13	ZKSCAN1	chr2:142888465-142889337	Hela-S3	cervix:	n/a	n/a
14	MAFK	chr2:142888897-142889314	HepG2	liver:	n/a	chr2:142889078-142889093 chr2:142889120-142889130 chr2:142889119-142889134 chr2:142889121-142889130
15	FOXA2	chr2:142889062-142889260	HepG2	liver:	n/a	n/a
16	MAFK	chr2:142888371-142889353	H1-hESC	embryonic stem cell:	n/a	chr2:142889078-142889093 chr2:142889120-142889130 chr2:142889119-142889134 chr2:142889121-142889130
17	POLR2A	chr2:142888237-142889210	H1-neurons	neurons:	n/a	n/a
18	CEBPB	chr2:142889061-142889366	ECC-1	luminal epithelium:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
19	GTF2F1	chr2:142888938-142889262	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr2:142888307-142889367	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr2:142888577-142889338	IMR90	lung:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
22	POLR2A	chr2:142888332-142889342	SK-N-MC	brain:	n/a	n/a
23	TAF1	chr2:142888993-142889251	Hela-S3	cervix:	n/a	n/a
24	USF2	chr2:142888627-142889171	Hela-S3	cervix:	n/a	n/a
25	GTF2F1	chr2:142888338-142889395	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr2:142888420-142889230	PFSK-1	brain:	n/a	n/a
27	RFX5	chr2:142888235-142889377	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr2:142888016-142889603	Hela-S3	cervix:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
29	KAP1	chr2:142887748-142889665	U2OS	brain:	n/a	n/a
30	POLR2A	chr2:142888181-142889335	Hela-S3	cervix:	n/a	n/a
31	ZNF143	chr2:142888403-142889255	Hela-S3	cervix:	n/a	n/a
32	SMARCC1	chr2:142887514-142889419	Hela-S3	cervix:	n/a	chr2:142889119-142889128
33	MAFF	chr2:142888832-142889308	HepG2	liver:	n/a	chr2:142889118-142889136
34	CEBPB	chr2:142888990-142889365	H1-hESC	embryonic stem cell:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
35	RAD21	chr2:142888790-142889278	H1-hESC	embryonic stem cell:	n/a	n/a
36	CHD2	chr2:142887910-142889313	Hela-S3	cervix:	n/a	n/a
37	EP300	chr2:142888487-142889373	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:142888230-142889413	U87	brain:	n/a	n/a
39	MYC	chr2:142888997-142889211	H1-hESC	embryonic stem cell:	n/a	n/a
40	SMARCB1	chr2:142887536-142889347	Hela-S3	cervix:	n/a	chr2:142889119-142889128
41	MAZ	chr2:142888885-142889358	Hela-S3	cervix:	n/a	n/a
42	SIN3A	chr2:142887607-142889256	H1-hESC	embryonic stem cell:	n/a	chr2:142888069-142888082
43	CEBPB	chr2:142888939-142889354	A549	lung:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
44	MAFK	chr2:142887872-142889379	Hela-S3	cervix:	n/a	chr2:142889078-142889093 chr2:142889120-142889130 chr2:142889119-142889134 chr2:142889121-142889130
45	POLR2A	chr2:142887608-142889138	H1-neurons	neurons:	n/a	n/a
46	KAP1	chr2:142887631-142889424	HEK293	kidney:	n/a	n/a
47	MAFF	chr2:142888983-142889303	K562	blood:	n/a	chr2:142889118-142889136
48	CEBPB	chr2:142888933-142889408	MCF-7	breast:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
49	POLR2A	chr2:142887609-142889307	MCF-7	breast:	n/a	n/a
50	RCOR1	chr2:142888295-142889446	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173835516..173837699-chr2:142887430..142889764,2	MCF-7	breast:

Variant related genes	Relation type
LRP1B	TF binding region
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10179879	0.81[CEU][hapmap]
rs10187861	0.81[EUR][1000 genomes]
rs10195203	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201177	0.90[CEU][hapmap]
rs11888082	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691633	0.81[CEU][hapmap]
rs12994651	0.81[CEU][hapmap]
rs13012748	0.81[CEU][hapmap]
rs13382235	0.84[CEU][hapmap]
rs13385180	0.81[CEU][hapmap]
rs13392919	0.90[CEU][hapmap]
rs13405280	0.81[CEU][hapmap]
rs13408738	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13418304	0.81[CEU][hapmap]
rs13420312	0.81[CEU][hapmap]
rs13432762	0.91[CHD][hapmap]
rs13432866	0.91[CHD][hapmap]
rs1349224	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449502	0.81[CEU][hapmap]
rs16847971	0.81[CEU][hapmap]
rs17832157	0.90[CEU][hapmap]
rs1982384	0.81[CEU][hapmap]
rs4662401	0.93[ASN][1000 genomes]
rs6721602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749591	0.81[CEU][hapmap]
rs7574284	0.81[CEU][hapmap]
rs7586590	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9630925	0.81[CEU][hapmap]
rs9653181	0.91[CHD][hapmap]

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	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142885400-142890800	Active TSS	Brain Anterior Caudate	brain
2	chr2:142885600-142890400	Active TSS	Brain Substantia Nigra	brain
3	chr2:142885800-142889800	Active TSS	Brain Angular Gyrus	brain
4	chr2:142885800-142890000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr2:142886000-142890000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:142887200-142889800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:142887400-142889200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:142887400-142889200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:142887400-142889200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:142887400-142889400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr2:142887400-142889400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:142887400-142889400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:142887400-142889400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:142887400-142889400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:142887400-142889600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr2:142887400-142889600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:142887400-142889600	Active TSS	Right Atrium	heart
18	chr2:142887600-142889200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:142887600-142889200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr2:142887600-142889200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
21	chr2:142887600-142889200	Bivalent/Poised TSS	Fetal Lung	lung
22	chr2:142887600-142889200	Active TSS	Gastric	stomach
23	chr2:142887600-142889200	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
25	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:142887600-142889400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:142887600-142889400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
30	chr2:142887600-142889400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr2:142887600-142889400	Flanking Active TSS	HMEC	breast
32	chr2:142887600-142889400	Active TSS	NHLF	lung
33	chr2:142887600-142889600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:142887600-142889600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:142887600-142889600	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr2:142887600-142889800	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr2:142887800-142889200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:142887800-142889200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:142887800-142889200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:142887800-142889200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
41	chr2:142887800-142889200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:142887800-142889200	Active TSS	Esophagus	oesophagus
43	chr2:142887800-142889200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr2:142887800-142889200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr2:142887800-142889200	Bivalent/Poised TSS	Thymus	Thymus
46	chr2:142887800-142889400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr2:142887800-142889400	Active TSS	Aorta	Aorta
48	chr2:142887800-142889400	Active TSS	Colon Smooth Muscle	Colon
49	chr2:142887800-142889400	Active TSS	Fetal Brain Male	brain
50	chr2:142887800-142889400	Active TSS	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links