Variant report

Variant	rs6721602
Chromosome Location	chr2:142889537-142889538
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	REST	chr2:142887426-142889581	H1-neurons	neurons:	n/a	chr2:142888105-142888115
2	POLR2A	chr2:142889523-142889684	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr2:142888016-142889603	Hela-S3	cervix:	n/a	chr2:142889168-142889177 chr2:142889168-142889177 chr2:142889168-142889177
4	KAP1	chr2:142887748-142889665	U2OS	brain:	n/a	n/a
5	BRCA1	chr2:142888764-142889594	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr2:142888218-142889588	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
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction

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

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

rs_ID	r²[population]
rs10164457	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]
rs10179879	0.81[CEU][hapmap]
rs10187861	0.81[EUR][1000 genomes]
rs10195203	0.88[AFR][1000 genomes];0.90[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[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];1.00[CHB][hapmap]
rs13385180	0.81[CEU][hapmap]
rs13392919	0.90[CEU][hapmap]
rs13405280	0.81[CEU][hapmap]
rs13408738	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13418304	0.81[CEU][hapmap]
rs13420312	0.81[CEU][hapmap]
rs13432762	0.90[CHD][hapmap];0.83[YRI][hapmap]
rs13432866	0.90[CHD][hapmap]
rs1349224	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[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]
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	0.90[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:41 , 50 per page) page: 1

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	chr2:142887400-142889600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:142887400-142889600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:142887400-142889600	Active TSS	Right Atrium	heart
10	chr2:142887600-142889600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:142887600-142889600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:142887600-142889600	Bivalent/Poised TSS	Fetal Kidney	kidney
13	chr2:142887600-142889800	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr2:142887800-142889600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:142887800-142889600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:142887800-142889600	Active TSS	Brain Cingulate Gyrus	brain
17	chr2:142887800-142889600	Bivalent/Poised TSS	A549	lung
18	chr2:142888000-142889600	Active TSS	Hela-S3	cervix
19	chr2:142888000-142889600	Active TSS	NH-A	brain
20	chr2:142888200-142889600	Active TSS	Fetal Brain Female	brain
21	chr2:142888800-142889600	Bivalent/Poised TSS	GM12878-XiMat	blood
22	chr2:142889000-142889600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr2:142889000-142889600	Active TSS	HUVEC	blood vessel
24	chr2:142889200-142889600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr2:142889200-142889600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:142889200-142889600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr2:142889200-142890800	Active TSS	Brain Hippocampus Middle	brain
28	chr2:142889200-142900800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:142889400-142889600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:142889400-142889600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:142889400-142889600	Bivalent Enhancer	Adipose Nuclei	Adipose
32	chr2:142889400-142889600	Enhancers	Liver	Liver
33	chr2:142889400-142889600	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:142889400-142889600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr2:142889400-142889600	Bivalent Enhancer	Fetal Intestine Large	intestine
36	chr2:142889400-142889600	Flanking Active TSS	Fetal Stomach	stomach
37	chr2:142889400-142889600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:142889400-142889600	Active TSS	HMEC	breast
39	chr2:142889400-142889600	Enhancers	Osteobl	bone
40	chr2:142889400-142889800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr2:142889400-142889800	Bivalent Enhancer	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links