Variant report

Variant	rs12988617
Chromosome Location	chr2:55465633-55465634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55464660..55467438-chr2:55495235..55498187,2	K562	blood:
2	chr2:55463258..55466209-chr2:55509433..55511989,3	MCF-7	breast:
3	chr2:55463171..55466180-chr2:55659869..55661423,3	MCF-7	breast:
4	chr2:55464242..55465805-chr2:55843421..55845196,2	MCF-7	breast:
5	chr2:55440554..55442948-chr2:55464620..55466638,2	MCF-7	breast:
6	chr17:56707291..56709390-chr2:55464798..55466329,2	MCF-7	breast:
7	chr2:55274511..55278444-chr2:55462893..55465890,4	K562	blood:
8	chr2:55464205..55466134-chr2:55493979..55496397,3	K562	blood:
9	chr2:55463589..55465767-chr2:55732207..55734884,2	MCF-7	breast:
10	chr2:55275648..55277729-chr2:55462893..55465890,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10200120	0.85[ASN][1000 genomes]
rs11357	0.84[ASN][1000 genomes]
rs11692206	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12052613	0.85[ASN][1000 genomes]
rs12615414	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12997656	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13021163	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17852670	0.91[ASN][1000 genomes]
rs2576712	0.80[ASN][1000 genomes]
rs2589080	0.85[ASN][1000 genomes]
rs2589100	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2864826	0.84[ASN][1000 genomes]
rs2917779	0.85[ASN][1000 genomes]
rs2920967	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34348115	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34511570	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4435493	0.91[ASN][1000 genomes]
rs56039135	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545480	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6706815	0.91[ASN][1000 genomes]
rs71414550	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72799507	0.80[ASN][1000 genomes]
rs934709	0.87[ASN][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12988617	CLHC1	cis	Artery Tibial	GTEx
rs12988617	CLHC1	cis	Adipose Subcutaneous	GTEx
rs12988617	CLHC1	cis	Esophagus Muscularis	GTEx
rs12988617	CLHC1	cis	Artery Aorta	GTEx
rs12988617	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs12988617	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs12988617	CLHC1	cis	Nerve Tibial	GTEx
rs12988617	CLHC1	cis	Whole Blood	GTEx
rs12988617	CLHC1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:55461400-55466600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55461600-55466600	Strong transcription	Fetal Intestine Large	intestine
5	chr2:55461600-55466600	Strong transcription	HSMMtube	muscle
6	chr2:55461600-55467400	Strong transcription	Adipose Nuclei	Adipose
7	chr2:55461600-55467800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:55461600-55469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:55461600-55471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
11	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
12	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
14	chr2:55461800-55465800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:55461800-55466600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr2:55461800-55467400	Strong transcription	Liver	Liver
17	chr2:55461800-55467400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:55461800-55472400	Weak transcription	Gastric	stomach
19	chr2:55461800-55472400	Weak transcription	Right Ventricle	heart
20	chr2:55461800-55474400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
23	chr2:55462000-55466600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:55462000-55467200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:55462000-55467400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:55462000-55467600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:55462000-55472600	Weak transcription	Fetal Heart	heart
28	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:55462200-55467600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:55462200-55473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
32	chr2:55462400-55466600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:55462400-55467000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:55462400-55467200	Strong transcription	HMEC	breast
35	chr2:55462400-55467400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:55462400-55476800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:55462400-55476800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr2:55462600-55466600	Strong transcription	Primary T cells from cord blood	blood
39	chr2:55462600-55466600	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr2:55462600-55467200	Strong transcription	NHDF-Ad	bronchial
41	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:55462800-55467800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:55463000-55466000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:55463000-55467000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:55463000-55467400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:55463000-55467800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:55463000-55477600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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