Variant report

Variant	rs59783675
Chromosome Location	chr2:55492154-55492155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55462896..55465238-chr2:55491054..55493846,2	MCF-7	breast:
2	chr2:55489175..55493124-chr2:55494672..55498680,8	MCF-7	breast:
3	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
4	chr2:55490801..55492846-chr2:55494879..55496493,2	K562	blood:
5	chr2:55481797..55485521-chr2:55489463..55492846,3	K562	blood:

Variant related genes	Relation type
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1821832	0.86[AMR][1000 genomes]
rs2576722	0.81[AMR][1000 genomes]
rs57681837	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59439819	0.91[AMR][1000 genomes]
rs61109509	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6726380	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7349360	0.91[AMR][1000 genomes]
rs7349405	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs59783675	CLHC1	cis	Artery Tibial	GTEx
rs59783675	CLHC1	cis	Whole Blood	GTEx
rs59783675	CLHC1	cis	Thyroid	GTEx
rs59783675	CLHC1	cis	Esophagus Muscularis	GTEx
rs59783675	CLHC1	cis	Artery Aorta	GTEx
rs59783675	CLHC1	cis	Muscle Skeletal	GTEx
rs59783675	CLHC1	cis	Adipose Subcutaneous	GTEx
rs59783675	CLHC1	cis	Stomach	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
5	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
18	chr2:55468800-55494400	Strong transcription	Liver	Liver
19	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:55472000-55495200	Weak transcription	Psoas Muscle	Psoas
22	chr2:55476000-55495400	Weak transcription	HUVEC	blood vessel
23	chr2:55476600-55495400	Weak transcription	Aorta	Aorta
24	chr2:55476600-55495400	Weak transcription	Fetal Heart	heart
25	chr2:55476600-55495600	Weak transcription	Esophagus	oesophagus
26	chr2:55476800-55495400	Weak transcription	Fetal Kidney	kidney
27	chr2:55478400-55493400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:55478400-55494800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55478800-55494200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:55479000-55493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:55480000-55495400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:55480400-55495600	Weak transcription	Brain Substantia Nigra	brain
33	chr2:55481400-55495400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:55481400-55495400	Weak transcription	Fetal Lung	lung
35	chr2:55481600-55495400	Weak transcription	NHDF-Ad	bronchial
36	chr2:55482800-55492400	Strong transcription	Left Ventricle	heart
37	chr2:55482800-55494600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:55483000-55494400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:55483000-55494600	Strong transcription	Fetal Intestine Small	intestine
40	chr2:55483000-55494600	Strong transcription	Fetal Stomach	stomach
41	chr2:55483200-55494800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:55483800-55492200	Strong transcription	Fetal Intestine Large	intestine
43	chr2:55484000-55493400	Strong transcription	HepG2	liver
44	chr2:55484000-55493600	Strong transcription	Placenta	Placenta
45	chr2:55484600-55492400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:55484600-55493400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:55484600-55493400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:55484600-55494400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:55484800-55494000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:55484800-55494400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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