Variant report

Variant	rs12694866
Chromosome Location	chr2:231284556-231284557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10165012	1.00[CHB][hapmap]
rs10170241	1.00[CHB][hapmap]
rs10207273	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694864	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694867	1.00[CHD][hapmap]
rs12694868	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694869	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397985	1.00[CHD][hapmap]
rs13413034	1.00[CHD][hapmap]
rs28445040	1.00[CHD][hapmap]
rs6707444	1.00[CHB][hapmap]
rs6710287	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6710297	1.00[CHD][hapmap]
rs6716753	1.00[CHD][hapmap]
rs6742304	1.00[CHB][hapmap]
rs6743984	1.00[CHD][hapmap]
rs7423615	1.00[CHD][hapmap]
rs9989899	1.00[CHD][hapmap]

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	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	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
rs12694866	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231281600-231294800	Weak transcription	Gastric	stomach
2	chr2:231281800-231284600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:231281800-231293000	Weak transcription	Fetal Stomach	stomach
4	chr2:231282000-231293400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:231282000-231294000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:231282200-231284800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr2:231282200-231285400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
8	chr2:231282400-231284800	Enhancers	Stomach Mucosa	stomach
9	chr2:231282400-231288600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:231282400-231292600	Weak transcription	A549	lung
11	chr2:231282600-231288600	Weak transcription	Fetal Intestine Large	intestine
12	chr2:231282600-231290000	Weak transcription	Placenta	Placenta
13	chr2:231283200-231284600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr2:231283200-231284600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:231283400-231284600	Enhancers	Primary hematopoietic stem cells	blood
16	chr2:231283400-231284600	Enhancers	Small Intestine	intestine
17	chr2:231283400-231284600	Enhancers	Spleen	Spleen
18	chr2:231283400-231285200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:231283400-231288400	Weak transcription	HepG2	liver
20	chr2:231283600-231284600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:231283600-231284600	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr2:231283600-231284600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr2:231283600-231284600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:231283600-231284600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:231283600-231287200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:231283600-231288600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:231283600-231288800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:231283600-231293800	Weak transcription	Fetal Lung	lung
29	chr2:231283600-231294800	Weak transcription	HSMM	muscle
30	chr2:231283600-231309200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:231283800-231284600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:231283800-231284600	Genic enhancers	Osteobl	bone
33	chr2:231283800-231285600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr2:231283800-231287000	Weak transcription	Aorta	Aorta
35	chr2:231283800-231287200	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:231283800-231288400	Weak transcription	K562	blood
37	chr2:231283800-231294600	Weak transcription	Fetal Heart	heart
38	chr2:231283800-231294800	Weak transcription	Esophagus	oesophagus
39	chr2:231284000-231284600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:231284000-231285200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:231284000-231287600	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:231284200-231284600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr2:231284200-231284600	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:231284200-231284600	Flanking Active TSS	Dnd41	blood
45	chr2:231284200-231284600	Active TSS	HMEC	breast
46	chr2:231284200-231284600	Enhancers	NHEK	skin
47	chr2:231284200-231284800	Enhancers	Adipose Nuclei	Adipose
48	chr2:231284200-231285000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:231284200-231285200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:231284200-231285200	Enhancers	Liver	Liver

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