Variant report

Variant	rs7301155
Chromosome Location	chr12:57622821-57622822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TFAP2A	chr12:57622778-57624185	Hela-S3	cervix:	n/a	chr12:57623801-57623815 chr12:57623310-57623321 chr12:57623310-57623321 chr12:57623310-57623321 chr12:57623309-57623323 chr12:57623311-57623326 chr12:57623309-57623323 chr12:57623310-57623321 chr12:57623330-57623345
2	POLR2A	chr12:57622661-57625191	U87	brain:	n/a	n/a
3	POLR2A	chr12:57622811-57628074	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:57622771-57623011	HCT-116	colon:	n/a	n/a
5	MXI1	chr12:57622692-57624810	IMR90	lung:	n/a	chr12:57623211-57623226
6	POLR2A	chr12:57622648-57625404	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr12:57622693-57625205	U87	brain:	n/a	n/a
8	MXI1	chr12:57622776-57624827	SK-N-SH	brain:	n/a	chr12:57623211-57623226
9	POLR2A	chr12:57622793-57623019	HepG2	liver:	n/a	n/a
10	TCF12	chr12:57622734-57624644	ECC-1	luminal epithelium:	n/a	chr12:57624361-57624368
11	SREBP1	chr12:57622746-57624168	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:57622758-57624862	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr12:57622817-57624181	GM18951	blood:	n/a	n/a
14	POLR2A	chr12:57622485-57625200	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr12:57622816-57624348	GM12891	blood:	n/a	n/a
16	CUX1	chr12:57622759-57623064	K562	blood:	n/a	n/a
17	RUNX3	chr12:57622748-57623825	GM12878	blood:	n/a	n/a
18	RELA	chr12:57622802-57624934	GM18951	blood:	n/a	n/a
19	POLR2A	chr12:57622615-57625235	IMR90	lung:	n/a	n/a
20	HCFC1	chr12:57622313-57625003	Hela-S3	cervix:	n/a	n/a
21	TFAP2C	chr12:57622801-57624230	Hela-S3	cervix:	n/a	chr12:57623799-57623814
22	RUNX3	chr12:57622785-57624352	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:57622801-57622851	NHDF-neo	bronchial:	n/a
2	chr12:57622801-57622851	A549	lung:	n/a
3	chr12:57622801-57622851	U87	brain:	n/a
4	chr12:57622801-57622851	HCPEpiC	choroid plexus:	n/a
5	chr12:57622801-57622851	GM19239	blood:	n/a
6	chr12:57622801-57622851	GM12892	blood:	n/a
7	chr12:57622801-57622851	NT2-D1	testis:	n/a
8	chr12:57622801-57622851	ProgFib	skin:	n/a
9	chr12:57622801-57622851	ovcar-3	ovarian:	n/a
10	chr12:57622801-57622851	PANC-1	pancreas:	n/a
11	chr12:57622801-57622851	HPAEpiC	pulmonary alveolar:	n/a
12	chr12:57622801-57622851	GM12878	blood:	n/a
13	chr12:57622801-57622851	HEK293	kidney:	embryo
14	chr12:57622801-57622851	SK-N-SH_RA	brain:	n/a
15	chr12:57622801-57622851	HIPEpiC	eye:	n/a
16	chr12:57622801-57622851	HMEC	breast:	n/a
17	chr12:57622801-57622851	AG04450	lung:	fetal
18	chr12:57622801-57622851	MCF-7	breast:	n/a
19	chr12:57622801-57622851	HRPEpiC	eye:	n/a
20	chr12:57622801-57622851	AG09319	gingival:	n/a
21	chr12:57622801-57622851	SK-N-SH	brain:	n/a
22	chr12:57622801-57622851	AG10803	skin:	n/a
23	chr12:57622801-57622851	AG09309	skin:	n/a
24	chr12:57622801-57622851	NH-A	brain:	n/a
25	chr12:57622801-57622851	IMR90	lung:	fetal
26	chr12:57622801-57622851	HL-60	blood:	n/a
27	chr12:57622801-57622851	NB4	blood:	n/a
28	chr12:57622801-57622851	HepG2	liver:	n/a
29	chr12:57622801-57622851	SKMC	muscle:	n/a
30	chr12:57622801-57622851	BJ	skin:	n/a
31	chr12:57622801-57622851	HCT-116	colon:	n/a
32	chr12:57622801-57622851	H1-hESC	embryonic stem cell:	embryo
33	chr12:57622801-57622851	HAEpiC	amniotic membrane:	n/a
34	chr12:57622801-57622851	HRCEpiC	kidney:	n/a
35	chr12:57622801-57622851	HCF	heart:	n/a
36	chr12:57622801-57622851	Hela-S3	cervix:	n/a
37	chr12:57622801-57622851	K562	blood:	n/a
38	chr12:57622801-57622851	Jurkat	blood:	n/a
39	chr12:57622801-57622851	BE2_C	brain:	n/a
40	chr12:57622801-57622851	HUVEC	blood vessel:	n/a
41	chr12:57622801-57622851	PFSK-1	brain:	n/a
42	chr12:57622801-57622851	Caco-2	colon:	n/a
43	chr12:57622801-57622851	HCM	heart:	n/a
44	chr12:57622801-57622851	HRE	kidney:	n/a
45	chr12:57622801-57622851	HNPCEpiC	eye:	n/a
46	chr12:57622801-57622851	ECC-1	luminal epithelium:	n/a
47	chr12:57622801-57622851	RPTEC	kidney:	n/a
48	chr12:57622801-57622851	LNCaP	prostate:	n/a
49	chr12:57622801-57622851	SAEC	small airway:	n/a
50	chr12:57622801-57622851	T-47D	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57480170..57482164-chr12:57622267..57624511,2	MCF-7	breast:
2	chr12:54673520..54675389-chr12:57621461..57623953,2	MCF-7	breast:
3	chr12:57622307..57625065-chr12:57914079..57916302,2	K562	blood:

No data

Variant related genes	Relation type
SHMT2	TF binding region
SHMT2	CpG island
ENSG00000166881	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000094916	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10783815	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs10783816	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1800164	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs68176600	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7311958	0.88[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs7489231	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7956957	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7978567	0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57611400-57623000	Weak transcription	Right Atrium	heart
2	chr12:57619800-57623000	Weak transcription	Gastric	stomach
3	chr12:57620600-57623400	Weak transcription	Pancreas	Pancrea
4	chr12:57621000-57623000	Weak transcription	Right Ventricle	heart
5	chr12:57621200-57623000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:57621200-57623000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:57621600-57623200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr12:57621600-57623200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:57621800-57623000	Enhancers	Primary hematopoietic stem cells	blood
10	chr12:57621800-57623000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:57621800-57623000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:57621800-57623000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:57621800-57623400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:57622400-57623000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:57622400-57623000	Enhancers	Primary B cells from cord blood	blood
16	chr12:57622400-57623000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:57622400-57623000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:57622400-57623000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:57622400-57623000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:57622400-57623000	Enhancers	NHDF-Ad	bronchial
21	chr12:57622400-57623200	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:57622600-57623000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:57622600-57623000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:57622600-57623000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:57622600-57623000	Enhancers	NH-A	brain
26	chr12:57622600-57623200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:57622600-57623200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:57622600-57623200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:57622600-57623200	Flanking Active TSS	Hela-S3	cervix
30	chr12:57622600-57623200	Flanking Bivalent TSS/Enh	HepG2	liver
31	chr12:57622600-57623400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:57622600-57623400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:57622600-57623400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:57622600-57623400	Bivalent Enhancer	Fetal Thymus	thymus
35	chr12:57622600-57623400	Flanking Active TSS	Dnd41	blood
36	chr12:57622600-57624800	Active TSS	HSMMtube	muscle
37	chr12:57622800-57623000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
38	chr12:57622800-57623000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr12:57622800-57623000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:57622800-57623000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
41	chr12:57622800-57623000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:57622800-57623000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:57622800-57623000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
44	chr12:57622800-57623000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
45	chr12:57622800-57623000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr12:57622800-57623000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:57622800-57623000	Enhancers	Adipose Nuclei	Adipose
48	chr12:57622800-57623000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:57622800-57623000	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr12:57622800-57623000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links