Variant report

Variant	rs12694864
Chromosome Location	chr2:231279221-231279222
allele	C/T
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	FOS	chr2:231279115-231279298	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:231279049-231279580	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231278937-231279296	GM12878	blood:	n/a	n/a
4	FOS	chr2:231279203-231279274	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10165012	1.00[CHB][hapmap]
rs10170241	1.00[CHB][hapmap]
rs10207273	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694866	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694868	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694869	1.00[ASN][1000 genomes]
rs13000381	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017297	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6707444	1.00[CHB][hapmap]
rs6710287	1.00[CHB][hapmap]
rs6742304	1.00[CHB][hapmap]

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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription 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	7 gene(s)	inside rSNPs	diseases
3	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12694864	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231277200-231279600	Weak transcription	NHDF-Ad	bronchial
2	chr2:231277200-231280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:231277200-231280400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:231277200-231280400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:231277200-231280400	Weak transcription	Aorta	Aorta
6	chr2:231277200-231280400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:231277200-231280400	Weak transcription	Psoas Muscle	Psoas
8	chr2:231277200-231280400	Weak transcription	Small Intestine	intestine
9	chr2:231277200-231280400	Weak transcription	HSMM	muscle
10	chr2:231277200-231280400	Weak transcription	HSMMtube	muscle
11	chr2:231277200-231280400	Weak transcription	NH-A	brain
12	chr2:231277200-231280800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:231277400-231279800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:231277400-231279800	Weak transcription	Osteobl	bone
15	chr2:231277400-231280000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:231277400-231280000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:231277400-231280200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:231277400-231280200	Enhancers	Primary T cells from cord blood	blood
19	chr2:231277400-231280200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:231277400-231280200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:231277400-231280200	Weak transcription	HUVEC	blood vessel
22	chr2:231277400-231280400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:231277400-231280400	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:231277400-231280400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr2:231277400-231280400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:231277400-231280400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr2:231277400-231280400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:231277400-231280400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:231277400-231280400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:231277400-231280400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:231277400-231280400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:231277400-231280400	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:231277400-231280400	Weak transcription	Fetal Lung	lung
34	chr2:231277400-231280400	Weak transcription	A549	lung
35	chr2:231277400-231280400	Enhancers	HepG2	liver
36	chr2:231277400-231280600	Weak transcription	Fetal Brain Male	brain
37	chr2:231277400-231280600	Weak transcription	Fetal Kidney	kidney
38	chr2:231277600-231279600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:231277600-231279800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:231277600-231279800	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:231277600-231279800	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:231277600-231279800	Weak transcription	Pancreas	Pancrea
43	chr2:231277600-231280000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:231277600-231280000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:231277600-231280200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:231277600-231280200	Weak transcription	Adipose Nuclei	Adipose
47	chr2:231277600-231280200	Weak transcription	Fetal Intestine Large	intestine
48	chr2:231277600-231280400	Enhancers	Primary B cells from cord blood	blood
49	chr2:231277600-231280400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:231277600-231280400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links