Variant report

Variant	rs10166038
Chromosome Location	chr2:127442846-127442847
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127426536..127429355-chr2:127441115..127443378,3	K562	blood:
2	chr2:127440013..127442980-chr2:127454337..127456567,2	K562	blood:
3	chr2:127434663..127437638-chr2:127440272..127442975,3	K562	blood:

Variant related genes	Relation type
ENSG00000235128	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13395599	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13398914	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17741655	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28387137	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28387146	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28387172	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28387177	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28387184	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002265	chr2:127029745-127733458	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535919	chr2:127029745-127733458	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583011	chr2:127386211-127489031	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875007	chr2:127426697-127454230	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10166038	CYP27C1	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127417200-127443600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:127422200-127453400	Weak transcription	Colonic Mucosa	Colon
3	chr2:127424200-127451000	Weak transcription	NHLF	lung
4	chr2:127424600-127447600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:127428000-127446400	Weak transcription	NHDF-Ad	bronchial
6	chr2:127430800-127444000	Weak transcription	Psoas Muscle	Psoas
7	chr2:127432800-127443400	Weak transcription	Thymus	Thymus
8	chr2:127433600-127451400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:127433800-127452600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:127434000-127446200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:127434000-127451000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:127434000-127451000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:127434200-127457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:127434400-127445400	Strong transcription	Fetal Stomach	stomach
15	chr2:127434800-127453000	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:127434800-127453200	Weak transcription	Placenta	Placenta
17	chr2:127435000-127445800	Weak transcription	Gastric	stomach
18	chr2:127435200-127444600	Weak transcription	Pancreas	Pancrea
19	chr2:127435200-127457400	Weak transcription	Fetal Kidney	kidney
20	chr2:127435400-127443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:127435400-127452800	Weak transcription	Fetal Intestine Large	intestine
22	chr2:127435600-127444800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:127435800-127444600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:127436000-127443400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr2:127436000-127444600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:127436400-127443000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:127436400-127444200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr2:127436600-127446000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:127436800-127446000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:127437200-127443600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:127437600-127443600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:127437600-127445000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:127437800-127444400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr2:127437800-127444600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:127439000-127447600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:127439600-127444400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:127439800-127443400	Weak transcription	Right Ventricle	heart
38	chr2:127439800-127457600	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:127440000-127443400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:127440200-127443800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:127440400-127447400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:127440400-127451200	Weak transcription	Esophagus	oesophagus
43	chr2:127440600-127444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:127440600-127447400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:127440800-127443400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:127441000-127443200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr2:127441000-127444000	Strong transcription	Ovary	ovary
48	chr2:127441000-127444600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:127441000-127446200	Weak transcription	HSMMtube	muscle
50	chr2:127441200-127444000	Strong transcription	Adipose Nuclei	Adipose

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