Variant report

Variant	rs1965584
Chromosome Location	chr12:56963259-56963260
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	TEAD4	chr12:56963163-56963554	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56959228..56960829-chr12:56962123..56963896,2	MCF-7	breast:
2	chr12:56582662..56585164-chr12:56962961..56964901,2	K562	blood:
3	chr12:56959480..56961532-chr12:56961606..56964152,2	K562	blood:

Variant related genes	Relation type
RBMS2	TF binding region
ENSG00000258199	Chromatin interaction
ENSG00000139613	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10747768	0.92[EUR][1000 genomes]
rs2939305	0.92[EUR][1000 genomes]
rs4237803	0.84[EUR][1000 genomes]
rs4237804	0.92[EUR][1000 genomes]
rs4547138	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv3375110	chr12:56956280-56965593	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv526706	chr12:56961932-56988342	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56931600-56965000	Weak transcription	Hela-S3	cervix
2	chr12:56948600-56981200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:56950800-56975000	Weak transcription	Esophagus	oesophagus
4	chr12:56951400-56963600	Weak transcription	Brain Anterior Caudate	brain
5	chr12:56952600-56966200	Weak transcription	Fetal Brain Female	brain
6	chr12:56952600-56974800	Weak transcription	Pancreas	Pancrea
7	chr12:56953200-56981200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:56954400-56974800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:56954600-56993400	Weak transcription	Fetal Brain Male	brain
10	chr12:56956000-56968800	Strong transcription	NHEK	skin
11	chr12:56956200-56970400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:56956600-56975000	Weak transcription	Gastric	stomach
13	chr12:56958400-56967400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:56959200-56964200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:56959400-56964800	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:56959400-56970000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:56959600-56963800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:56959600-56975000	Weak transcription	Right Ventricle	heart
19	chr12:56959800-56963400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:56959800-56963600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:56959800-56963600	Enhancers	Fetal Intestine Small	intestine
22	chr12:56959800-56970400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:56959800-56971800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:56959800-56974800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:56959800-56975000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:56959800-56981400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:56960000-56963400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:56960000-56963400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:56960000-56963400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:56960000-56963400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:56960000-56963600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:56960000-56963600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:56960000-56963600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:56960000-56963600	Weak transcription	Right Atrium	heart
35	chr12:56960000-56963600	Weak transcription	Stomach Mucosa	stomach
36	chr12:56960000-56963600	Weak transcription	Spleen	Spleen
37	chr12:56960000-56963800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:56960000-56967400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:56960000-56968000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:56960000-56974800	Weak transcription	Aorta	Aorta
41	chr12:56960000-56975000	Weak transcription	Small Intestine	intestine
42	chr12:56960000-56975200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:56960000-56975800	Weak transcription	Colonic Mucosa	Colon
44	chr12:56960000-56976000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:56960000-56981000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:56960000-56981200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:56960000-56981200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:56960000-56981200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:56960000-56981200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:56960000-56987600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links