Variant report

Variant	rs11125556
Chromosome Location	chr2:55383107-55383108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55366215..55370139-chr2:55381125..55383848,4	K562	blood:
2	chr2:55378428..55381284-chr2:55382487..55384417,2	MCF-7	breast:
3	chr2:55381461..55384180-chr2:55385114..55387794,2	MCF-7	breast:
4	chr2:18390509..18393280-chr2:55382468..55384962,2	MCF-7	breast:
5	chr2:55272933..55279731-chr2:55382949..55387132,8	K562	blood:
6	chr2:55275348..55277918-chr2:55382981..55385901,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11125555	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1133181	0.83[CHB][hapmap]
rs12470651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621144	0.83[CHB][hapmap]
rs12623137	0.80[JPT][hapmap]
rs12990898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576711	0.86[JPT][hapmap]
rs2589096	0.85[JPT][hapmap]
rs3935223	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs4672024	0.83[CHB][hapmap]
rs4672025	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672026	0.80[ASN][1000 genomes]
rs6545475	0.81[CHB][hapmap]
rs66483070	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715130	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7568777	0.86[AMR][1000 genomes]
rs7595134	0.82[CHB][hapmap]
rs7608118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11125556	CLHC1	cis	lung	GTEx
rs11125556	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs11125556	C2orf63	cis	Lymphoblastoid	GTEx
rs11125556	CLHC1	cis	Whole Blood	GTEx
rs11125556	CLHC1	cis	Artery Tibial	GTEx
rs11125556	CLHC1	cis	Thyroid	GTEx
rs11125556	CLHC1	cis	Adipose Subcutaneous	GTEx
rs11125556	CLHC1	cis	Muscle Skeletal	GTEx
rs11125556	FLJ31438	cis	multi-tissue	Pritchard
rs11125556	CLHC1	cis	Nerve Tibial	GTEx
rs11125556	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:55378200-55383600	Enhancers	Brain Substantia Nigra	brain
5	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
6	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
7	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose
8	chr2:55378400-55383800	Enhancers	NHLF	lung
9	chr2:55378600-55383200	Enhancers	Colon Smooth Muscle	Colon
10	chr2:55378600-55383600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:55378600-55385600	Enhancers	Rectal Smooth Muscle	rectum
12	chr2:55378600-55386800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr2:55378600-55386800	Enhancers	Fetal Stomach	stomach
14	chr2:55378800-55383200	Enhancers	Fetal Brain Male	brain
15	chr2:55378800-55383600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:55378800-55385600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:55378800-55386800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:55379000-55384200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:55379200-55383600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:55379200-55385200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:55379400-55385200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:55379400-55386600	Enhancers	Fetal Intestine Large	intestine
23	chr2:55379400-55387000	Enhancers	Fetal Intestine Small	intestine
24	chr2:55379600-55385000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:55379600-55386800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:55380000-55384400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:55380200-55386000	Enhancers	Hela-S3	cervix
28	chr2:55380400-55384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:55380600-55383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:55380600-55384000	Enhancers	Fetal Heart	heart
31	chr2:55380600-55384000	Enhancers	HMEC	breast
32	chr2:55380800-55383400	Enhancers	NHDF-Ad	bronchial
33	chr2:55380800-55383600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:55380800-55385400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:55381000-55383600	Enhancers	HSMM	muscle
36	chr2:55381000-55384400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:55381000-55387800	Enhancers	Fetal Muscle Leg	muscle
38	chr2:55381000-55391000	Enhancers	Stomach Mucosa	stomach
39	chr2:55381200-55390600	Enhancers	Brain Angular Gyrus	brain
40	chr2:55381400-55383200	Enhancers	Brain Anterior Caudate	brain
41	chr2:55381400-55385600	Enhancers	Brain Germinal Matrix	brain
42	chr2:55381600-55383400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:55381600-55383600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:55381600-55383800	Weak transcription	Fetal Thymus	thymus
45	chr2:55381600-55386800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:55381600-55386800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:55381800-55384400	Weak transcription	GM12878-XiMat	blood
48	chr2:55381800-55385200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:55381800-55385600	Enhancers	NHEK	skin
50	chr2:55381800-55387200	Enhancers	Skeletal Muscle Female	skeletal muscle

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