Variant report

Variant	rs12487600
Chromosome Location	chr3:196046404-196046405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:196045858-196046408	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr3:196045876-196046738	K562	blood:	n/a	n/a
3	POLR2A	chr3:196043571-196047499	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:196046217-196046738	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:196045875-196046737	K562	blood:	n/a	n/a
6	POLR2A	chr3:196046229-196046754	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:196044281-196047616	K562	blood:	n/a	n/a
8	POLR2A	chr3:196046257-196046646	HCT-116	colon:	n/a	n/a
9	POLR2A	chr3:196046195-196046468	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:196046371-196046423	Hela-S3	cervix:	n/a	n/a
11	HEY1	chr3:196045880-196046414	K562	blood:	n/a	n/a
12	POLR2A	chr3:196044333-196046786	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196044828..196047817-chr3:196050115..196053393,5	K562	blood:
2	chr3:196043015..196047197-chr3:196061951..196068288,11	K562	blood:
3	chr3:196043730..196046568-chr3:196064807..196067685,4	MCF-7	breast:
4	chr3:196012377..196016502-chr3:196041586..196047553,11	K562	blood:
5	chr3:196022549..196024808-chr3:196044443..196046676,2	K562	blood:
6	chr3:196012669..196015162-chr3:196043820..196046764,2	K562	blood:
7	chr3:196045968..196048750-chr3:196049262..196052287,4	K562	blood:
8	chr3:196043702..196046805-chr3:196047566..196053193,12	MCF-7	breast:
9	chr3:196040934..196046683-chr3:196067954..196076269,13	MCF-7	breast:
10	chr3:196045621..196048927-chr3:196067958..196070489,3	MCF-7	breast:
11	chr3:196043015..196046706-chr3:196061951..196066451,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272741	TF binding region
TCTEX1D2	TF binding region
ENSG00000212146	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000145107	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12490110	0.81[AFR][1000 genomes]
rs12497601	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1357289	0.85[AFR][1000 genomes]
rs2280526	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916480	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56346343	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56393817	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56845593	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60670584	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61134797	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61615159	0.82[AFR][1000 genomes]
rs67127834	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67581262	0.89[ASN][1000 genomes]
rs6777819	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6779233	0.90[ASN][1000 genomes]
rs6782336	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67844518	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785339	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73212183	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7616515	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7631913	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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 miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
6	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
9	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
16	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
17	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
18	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
20	nsv4183	chr3:196034067-196079109	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12487600	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs12487600	TM4SF19	cis	Muscle Skeletal	GTEx
rs12487600	SLC51A	cis	Heart Left Ventricle	GTEx
rs12487600	TM4SF19-AS1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196043600-196046600	Active TSS	A549	lung
2	chr3:196043800-196047000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:196045600-196046600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:196045600-196048600	Weak transcription	Thymus	Thymus
5	chr3:196045600-196053800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:196045600-196054000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:196045600-196054000	Weak transcription	Pancreas	Pancrea
8	chr3:196045600-196054200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:196045600-196054200	Weak transcription	Ovary	ovary
10	chr3:196045800-196046600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:196045800-196046600	Enhancers	Fetal Thymus	thymus
12	chr3:196045800-196047000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:196045800-196047000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:196045800-196047200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:196045800-196047600	Enhancers	Fetal Muscle Trunk	muscle
16	chr3:196045800-196047600	Enhancers	Spleen	Spleen
17	chr3:196045800-196047600	Enhancers	NHEK	skin
18	chr3:196045800-196052400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:196045800-196052800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:196045800-196053000	Weak transcription	Fetal Intestine Small	intestine
21	chr3:196045800-196054200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:196046000-196046600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:196046000-196046600	Enhancers	Adipose Nuclei	Adipose
24	chr3:196046000-196046600	ZNF genes & repeats	K562	blood
25	chr3:196046000-196047000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:196046000-196047200	Weak transcription	Placenta	Placenta
27	chr3:196046000-196047400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:196046000-196047600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:196046000-196047600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:196046000-196047600	Enhancers	HMEC	breast
31	chr3:196046000-196050200	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:196046000-196050800	Weak transcription	HSMM	muscle
33	chr3:196046000-196053600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:196046000-196054400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:196046200-196046600	Enhancers	Dnd41	blood
36	chr3:196046200-196046800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr3:196046200-196047200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:196046200-196050600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:196046200-196051000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:196046200-196054200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:196046400-196046600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:196046400-196046600	Enhancers	Hela-S3	cervix
43	chr3:196046400-196046600	Flanking Active TSS	HepG2	liver
44	chr3:196046400-196046600	Enhancers	NH-A	brain
45	chr3:196046400-196047400	Enhancers	HUVEC	blood vessel
46	chr3:196046400-196047400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:196046400-196047600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:196046400-196047600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:196046400-196047600	Enhancers	Esophagus	oesophagus
50	chr3:196046400-196048800	Weak transcription	Primary T cells fromperipheralblood	blood

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