Variant report

Variant	rs61109509
Chromosome Location	chr2:55471382-55471383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55424063..55425912-chr2:55471234..55472747,2	K562	blood:
2	chr2:55468207..55471857-chr2:55475862..55479587,5	K562	blood:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17046778	0.95[ASN][1000 genomes]
rs1821832	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2576722	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2920965	0.91[ASN][1000 genomes]
rs57529275	0.89[ASN][1000 genomes]
rs57681837	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59439819	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59783675	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61486882	0.83[ASN][1000 genomes]
rs6726380	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7349360	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7349405	0.92[AMR][1000 genomes];0.83[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs61109509	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs61109509	C2orf63	cis	multi-tissue	Pritchard
rs61109509	CLHC1	cis	Adipose Subcutaneous	GTEx
rs61109509	CLHC1	cis	Heart Left Ventricle	GTEx
rs61109509	CLHC1	cis	Artery Aorta	GTEx
rs61109509	CLHC1	cis	Muscle Skeletal	GTEx
rs61109509	CLHC1	cis	Esophagus Muscularis	GTEx
rs61109509	CLHC1	cis	Thyroid	GTEx
rs61109509	CLHC1	cis	Stomach	GTEx
rs61109509	CLHC1	cis	Whole Blood	GTEx
rs61109509	CLHC1	cis	Artery Tibial	GTEx
rs61109509	CLHC1	cis	lung	GTEx
rs61109509	CLHC1	cis	Nerve Tibial	GTEx
rs61109509	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55461600-55471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
4	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
5	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
7	chr2:55461800-55472400	Weak transcription	Gastric	stomach
8	chr2:55461800-55472400	Weak transcription	Right Ventricle	heart
9	chr2:55461800-55474400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
12	chr2:55462000-55472600	Weak transcription	Fetal Heart	heart
13	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:55462200-55473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
16	chr2:55462400-55476800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:55462400-55476800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:55463000-55477600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:55463200-55481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:55463400-55472400	Weak transcription	Lung	lung
25	chr2:55463400-55472400	Weak transcription	Ovary	ovary
26	chr2:55463400-55474200	Weak transcription	Aorta	Aorta
27	chr2:55463400-55475800	Weak transcription	Spleen	Spleen
28	chr2:55463400-55488200	Weak transcription	Pancreas	Pancrea
29	chr2:55463600-55472400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:55463600-55474800	Weak transcription	Thymus	Thymus
31	chr2:55463600-55483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:55463800-55471600	Weak transcription	Psoas Muscle	Psoas
33	chr2:55463800-55475400	Weak transcription	Esophagus	oesophagus
34	chr2:55463800-55479600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:55463800-55486200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:55464000-55476200	Weak transcription	Fetal Kidney	kidney
40	chr2:55464200-55473600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:55464400-55472400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:55464400-55472400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:55464400-55476200	Weak transcription	Brain Angular Gyrus	brain
44	chr2:55464400-55479600	Weak transcription	NHLF	lung
45	chr2:55464600-55475600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:55464600-55476200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:55464600-55476200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:55464600-55479400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:55464800-55472600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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