Variant report

Variant	rs1454932
Chromosome Location	chr12:32909846-32909847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:32909800-32909950	BE2_C	brain:	n/a	n/a
2	RAD21	chr12:32907257-32910251	SK-N-SH	brain:	n/a	chr12:32909329-32909348
3	SMC3	chr12:32907892-32910060	Hela-S3	cervix:	n/a	chr12:32909330-32909344
4	CTCF	chr12:32907767-32910220	A549	lung:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
5	KAP1	chr12:32907724-32909921	HEK293	kidney:	n/a	n/a
6	SMC3	chr12:32907727-32910149	SK-N-SH	brain:	n/a	chr12:32909330-32909344
7	CTCF	chr12:32907735-32910118	SK-N-SH	brain:	n/a	chr12:32909330-32909351 chr12:32909331-32909344 chr12:32909328-32909346
8	CTCF	chr12:32909800-32909950	HFF-Myc	foreskin:	n/a	n/a
9	FOS	chr12:32909429-32910082	HUVEC	blood vessel:	n/a	chr12:32909451-32909458 chr12:32909525-32909534

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:32909796-32909846	HCF	heart:	n/a
2	chr12:32909796-32909846	HRE	kidney:	n/a
3	chr12:32909796-32909846	SK-N-SH_RA	brain:	n/a
4	chr12:32909796-32909846	AoSMC	blood vessel:	n/a
5	chr12:32909796-32909846	IMR90	lung:	fetal
6	chr12:32909796-32909846	ECC-1	luminal epithelium:	n/a
7	chr12:32909796-32909846	SK-N-SH	brain:	n/a
8	chr12:32909796-32909846	HUVEC	blood vessel:	n/a
9	chr12:32909796-32909846	HPAEpiC	pulmonary alveolar:	n/a
10	chr12:32909796-32909846	HCT-116	colon:	n/a
11	chr12:32909796-32909846	ovcar-3	ovarian:	n/a
12	chr12:32909796-32909846	AG04449	skin:	fetal
13	chr12:32909796-32909846	HL-60	blood:	n/a
14	chr12:32909796-32909846	CMK	blood:	n/a
15	chr12:32909796-32909846	HCM	heart:	n/a
16	chr12:32909796-32909846	GM12878	blood:	n/a
17	chr12:32909796-32909846	H1-hESC	embryonic stem cell:	embryo
18	chr12:32909796-32909846	PANC-1	pancreas:	n/a
19	chr12:32909796-32909846	Hepatocyte	liver:	n/a
20	chr12:32909796-32909846	NHBE	bronchial:	n/a
21	chr12:32909796-32909846	BE2_C	brain:	n/a
22	chr12:32909796-32909846	AG04450	lung:	fetal
23	chr12:32909796-32909846	Hela-S3	cervix:	n/a
24	chr12:32909796-32909846	ProgFib	skin:	n/a
25	chr12:32909796-32909846	NH-A	brain:	n/a
26	chr12:32909796-32909846	PrEC	prostate:	n/a
27	chr12:32909796-32909846	NHDF-neo	bronchial:	n/a
28	chr12:32909796-32909846	HEK293	kidney:	embryo
29	chr12:32909796-32909846	T-47D	breast:	n/a
30	chr12:32909796-32909846	MCF10A-Er-Src	breast:	n/a
31	chr12:32909796-32909846	GM19239	blood:	n/a
32	chr12:32909796-32909846	K562	blood:	n/a
33	chr12:32909796-32909846	HepG2	liver:	n/a
34	chr12:32909796-32909846	SAEC	small airway:	n/a
35	chr12:32909796-32909846	MCF-7	breast:	n/a
36	chr12:32909796-32909846	SK-N-MC	brain:	n/a
37	chr12:32909796-32909846	AG09309	skin:	n/a
38	chr12:32909796-32909846	RPTEC	kidney:	n/a
39	chr12:32909796-32909846	A549	lung:	n/a
40	chr12:32909796-32909846	HAEpiC	amniotic membrane:	n/a
41	chr12:32909796-32909846	HMEC	breast:	n/a
42	chr12:32909796-32909846	Caco-2	colon:	n/a
43	chr12:32909796-32909846	Jurkat	blood:	n/a
44	chr12:32909796-32909846	HNPCEpiC	eye:	n/a
45	chr12:32909796-32909846	GM12891	blood:	n/a
46	chr12:32909796-32909846	GM12892	blood:	n/a
47	chr12:32909796-32909846	PFSK-1	brain:	n/a
48	chr12:32909796-32909846	HRCEpiC	kidney:	n/a
49	chr12:32909796-32909846	HCPEpiC	choroid plexus:	n/a
50	chr12:32909796-32909846	LNCaP	prostate:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:32907107..32909879-chr12:32974270..32975942,2	K562	blood:
2	chr12:32909198..32910124-chr12:33071777..33072639,3	MCF-7	breast:
3	chr12:32908900..32910812-chr12:32911585..32914530,2	K562	blood:
4	chr12:32908990..32910670-chr12:34173573..34175511,2	K562	blood:
5	chr12:32832004..32833946-chr12:32906988..32909887,3	MCF-7	breast:
6	chr12:32909522..32911268-chr12:33072253..33074480,2	MCF-7	breast:
7	chr12:32902299..32904984-chr12:32908343..32910409,2	K562	blood:
8	chr12:32908157..32910268-chr12:33048253..33050625,4	MCF-7	breast:

No data

Variant related genes	Relation type
YARS2	TF binding region
YARS2	CpG island
ENSG00000139133	Chromatin interaction
ENSG00000139131	Chromatin interaction
ENSG00000087470	Chromatin interaction
ENSG00000057294	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1020670	0.87[ASN][1000 genomes]
rs10771978	0.84[CHD][hapmap]
rs10771984	0.89[ASW][hapmap];0.84[CHD][hapmap]
rs10771988	0.87[ASN][1000 genomes]
rs10771989	0.87[ASN][1000 genomes]
rs10844300	0.89[ASW][hapmap];0.84[CHD][hapmap]
rs10844309	0.84[CHD][hapmap]
rs10844318	0.82[CHD][hapmap]
rs10844321	0.82[ASN][1000 genomes]
rs10844322	0.82[ASN][1000 genomes]
rs10844324	1.00[ASW][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs10844326	0.82[ASN][1000 genomes]
rs10844328	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs10844329	0.82[ASN][1000 genomes]
rs10844330	0.89[ASW][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs10844332	0.87[ASN][1000 genomes]
rs10844333	0.87[ASN][1000 genomes]
rs10844334	0.87[ASN][1000 genomes]
rs10844335	0.87[ASN][1000 genomes]
rs10844336	0.87[ASN][1000 genomes]
rs10844337	0.89[ASW][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs10844338	0.87[ASN][1000 genomes]
rs10844339	0.87[ASN][1000 genomes]
rs10844340	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052168	0.89[ASW][hapmap];0.84[CHD][hapmap]
rs11052176	0.89[ASW][hapmap];0.82[CHD][hapmap]
rs11052177	0.84[CHD][hapmap]
rs11052179	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs11052197	0.84[CHD][hapmap]
rs11052198	0.89[ASW][hapmap];0.84[CHD][hapmap]
rs11052199	0.84[CHD][hapmap]
rs11052205	0.82[ASN][1000 genomes]
rs11052206	0.82[ASN][1000 genomes]
rs11052210	0.87[ASN][1000 genomes]
rs11052211	0.87[ASN][1000 genomes]
rs11052213	0.87[ASN][1000 genomes]
rs11052214	0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs11052217	0.87[ASN][1000 genomes]
rs11539444	0.87[ASN][1000 genomes]
rs11539445	0.87[ASN][1000 genomes]
rs11830934	0.81[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12317270	0.84[CHD][hapmap]
rs12320877	0.82[ASN][1000 genomes]
rs17541794	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1971911	0.89[ASW][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2030747	0.87[ASN][1000 genomes]
rs2124150	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2124151	0.87[ASN][1000 genomes]
rs2272238	0.87[ASW][hapmap]
rs28464612	0.82[ASN][1000 genomes]
rs3809232	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827883	0.87[ASN][1000 genomes]
rs4539413	0.89[ASW][hapmap];0.82[CHD][hapmap]
rs58669264	0.82[ASN][1000 genomes]
rs61328017	0.82[ASN][1000 genomes]
rs61454222	0.82[ASN][1000 genomes]
rs6488080	0.82[ASN][1000 genomes]
rs7135097	0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs7294800	0.89[ASN][1000 genomes]
rs7294844	0.86[ASN][1000 genomes]
rs7295181	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7298030	0.82[CHD][hapmap]
rs7302970	0.84[CHD][hapmap]
rs7306406	0.89[ASW][hapmap];0.82[CHD][hapmap]
rs73082829	0.82[AMR][1000 genomes]
rs73088891	0.87[ASN][1000 genomes]
rs7310136	0.82[ASN][1000 genomes]
rs7311316	0.86[ASN][1000 genomes]
rs7954322	0.87[ASN][1000 genomes]
rs7955582	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7957603	0.87[ASN][1000 genomes]
rs7957841	0.89[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7969353	0.87[ASN][1000 genomes]
rs977542	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1051667	chr12:32871860-32919673	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1042661	chr12:32871860-32928833	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1050779	chr12:32872999-32921973	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr12:32909400-32910000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:32909400-32910000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:32909400-32910000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:32909400-32910000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:32909400-32910000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:32909400-32910000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:32909400-32910000	Enhancers	Duodenum Mucosa	Duodenum
8	chr12:32909400-32910000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:32909400-32910000	Enhancers	Fetal Intestine Small	intestine
10	chr12:32909400-32910000	Enhancers	Placenta	Placenta
11	chr12:32909400-32910000	Flanking Active TSS	HepG2	liver
12	chr12:32909400-32910200	Enhancers	Fetal Heart	heart
13	chr12:32909400-32910400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:32909400-32910600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:32909400-32910600	Enhancers	Fetal Intestine Large	intestine
16	chr12:32909400-32914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:32909600-32910000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:32909600-32910000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:32909600-32910000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:32909600-32910000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:32909600-32910000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr12:32909600-32910000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:32909600-32910000	Enhancers	Brain Cingulate Gyrus	brain
24	chr12:32909600-32910000	Enhancers	Colon Smooth Muscle	Colon
25	chr12:32909600-32910000	Enhancers	Left Ventricle	heart
26	chr12:32909600-32910000	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr12:32909600-32910000	Enhancers	Dnd41	blood
28	chr12:32909600-32910000	Enhancers	HMEC	breast
29	chr12:32909600-32910000	Enhancers	NH-A	brain
30	chr12:32909600-32910000	Enhancers	NHDF-Ad	bronchial
31	chr12:32909600-32910000	Enhancers	NHEK	skin
32	chr12:32909600-32910200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:32909600-32910600	Enhancers	Fetal Lung	lung
34	chr12:32909600-32914200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:32909600-32914200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:32909600-32914200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:32909600-32914400	Weak transcription	GM12878-XiMat	blood
38	chr12:32909800-32910000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:32909800-32912000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:32909800-32914200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:32909800-32914200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links