Variant report

Variant	rs1161187
Chromosome Location	chr12:67836590-67836591
allele	C/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	NFIC	chr12:67835344-67836716	ECC-1	luminal epithelium:	n/a	n/a
2	RFX5	chr12:67834796-67836630	IMR90	lung:	n/a	chr12:67835776-67835791 chr12:67836334-67836342
3	KAP1	chr12:67836364-67836720	U2OS	brain:	n/a	n/a
4	GATA2	chr12:67835436-67836916	SH-SY5Y	brain:	n/a	chr12:67835668-67835678 chr12:67836540-67836561 chr12:67835557-67835578 chr12:67835559-67835575
5	RFX5	chr12:67834712-67837907	SK-N-SH	brain:	n/a	chr12:67835776-67835791 chr12:67836334-67836342
6	RAD21	chr12:67835136-67837011	SK-N-SH	brain:	n/a	chr12:67835739-67835758 chr12:67835745-67835754 chr12:67836697-67836707 chr12:67836258-67836270
7	SMC3	chr12:67835472-67836753	SK-N-SH	brain:	n/a	chr12:67836448-67836455 chr12:67836697-67836707 chr12:67835743-67835757
8	GATA3	chr12:67836279-67837102	SH-SY5Y	brain:	n/a	chr12:67836540-67836561
9	CTCF	chr12:67835358-67836945	SK-N-SH	brain:	n/a	chr12:67835743-67835756 chr12:67835743-67835756 chr12:67835742-67835758 chr12:67835736-67835757 chr12:67835741-67835759
10	GATA3	chr12:67836180-67836690	SK-N-SH	brain:	n/a	chr12:67836540-67836561
11	NFIC	chr12:67835451-67836731	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr12:67836282-67836640	SK-N-SH_RA	brain:	n/a	n/a
13	GATA3	chr12:67836110-67836730	SK-N-SH	brain:	n/a	chr12:67836540-67836561

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67835015..67836626-chr12:68041629..68043874,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIP1-4	chr12:67836568-67836838	XLOC_010112
2	lnc-GRIP1-4	chr12:67836567-67836838	NONHSAT029254

Variant related genes	Relation type
ENSG00000256172	TF binding region
ENSG00000127334	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1161106	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1161110	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1161188	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1183493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1613130	0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17103860	0.81[EUR][1000 genomes]
rs17103862	0.81[EUR][1000 genomes]
rs17120722	0.83[EUR][1000 genomes]
rs1732626	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67831000-67836600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:67835000-67836600	Enhancers	Duodenum Smooth Muscle	Duodenum
3	chr12:67835000-67836800	Enhancers	Stomach Mucosa	stomach
4	chr12:67835000-67837000	Enhancers	Fetal Heart	heart
5	chr12:67835200-67836600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:67835200-67836600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr12:67835200-67836800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:67835200-67836800	Enhancers	Fetal Intestine Large	intestine
9	chr12:67835200-67836800	Enhancers	Fetal Intestine Small	intestine
10	chr12:67835200-67836800	Enhancers	Fetal Muscle Leg	muscle
11	chr12:67835200-67836800	Enhancers	HSMM	muscle
12	chr12:67835200-67837000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr12:67835200-67837200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:67835400-67836600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:67835400-67836600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:67835400-67836600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:67835400-67836600	Enhancers	Fetal Thymus	thymus
18	chr12:67835400-67836600	Enhancers	NH-A	brain
19	chr12:67835400-67836800	Enhancers	Liver	Liver
20	chr12:67835400-67836800	Enhancers	Brain Angular Gyrus	brain
21	chr12:67835400-67837000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:67835400-67837000	Enhancers	Brain Germinal Matrix	brain
23	chr12:67835400-67837000	Enhancers	Fetal Lung	lung
24	chr12:67835600-67836600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:67835600-67836600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:67835600-67836600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:67835600-67836600	Enhancers	Thymus	Thymus
28	chr12:67835600-67837000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:67835600-67837000	Enhancers	Fetal Muscle Trunk	muscle
30	chr12:67835600-67837000	Enhancers	Right Ventricle	heart
31	chr12:67835600-67849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:67835800-67836600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:67835800-67836600	Enhancers	Fetal Stomach	stomach
34	chr12:67835800-67836600	Bivalent Enhancer	HepG2	liver
35	chr12:67835800-67836800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:67835800-67837200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:67836000-67837200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:67836000-67840800	Weak transcription	Primary T cells from cord blood	blood
39	chr12:67836200-67836600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:67836200-67836600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr12:67836200-67836600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:67836200-67836600	Enhancers	Fetal Brain Male	brain
43	chr12:67836200-67836600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr12:67836200-67836800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:67836200-67837000	Enhancers	Aorta	Aorta
46	chr12:67836200-67837000	Enhancers	Fetal Brain Female	brain
47	chr12:67836200-67837400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:67836400-67836600	Active TSS	Colonic Mucosa	Colon
49	chr12:67836400-67836600	Enhancers	Duodenum Mucosa	Duodenum
50	chr12:67836400-67836600	Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links