Variant report

Variant	rs2252920
Chromosome Location	chr6:37418327-37418328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37400708..37403297-chr6:37418149..37420287,2	K562	blood:
2	chr6:37416543..37419137-chr6:37419847..37423268,4	K562	blood:
3	chr6:37417610..37419144-chr6:37423801..37425835,2	K562	blood:
4	chr6:37346641..37348190-chr6:37418014..37420567,2	K562	blood:
5	chr6:37416658..37419245-chr6:37423561..37426187,3	MCF-7	breast:
6	chr6:37416282..37419426-chr6:37419538..37422367,4	MCF-7	breast:
7	chr6:37369587..37371664-chr6:37416739..37419085,2	K562	blood:

Variant related genes	Relation type
ENSG00000137200	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10692	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947673	0.82[CHB][hapmap]
rs11756941	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs12212090	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1224127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1224128	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1224129	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812186	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2646926	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2646933	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2646934	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2776881	0.91[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2776906	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2776908	0.86[ASN][1000 genomes]
rs2776910	0.86[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2776911	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs2776916	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2797790	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4257849	0.97[ASN][1000 genomes]
rs62406516	0.89[ASN][1000 genomes]
rs756202	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs904251	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs931649	0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2252920	RP1-153P14.5	cis	Whole Blood	GTEx
rs2252920	RP1-153P14.8	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37402200-37427800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:37403000-37434400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:37403200-37418400	Strong transcription	Fetal Stomach	stomach
4	chr6:37403200-37422000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:37403200-37423800	Strong transcription	Fetal Thymus	thymus
6	chr6:37403200-37432000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:37403200-37432600	Strong transcription	Placenta	Placenta
8	chr6:37403200-37433200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:37403400-37422000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:37403400-37423800	Strong transcription	K562	blood
11	chr6:37403400-37432000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:37408800-37433400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:37409200-37426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:37410000-37422200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:37410400-37432400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:37410600-37434200	Strong transcription	Primary T cells from cord blood	blood
17	chr6:37411200-37422000	Weak transcription	Right Atrium	heart
18	chr6:37411200-37428200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:37411200-37431400	Strong transcription	GM12878-XiMat	blood
20	chr6:37411200-37432800	Strong transcription	Primary B cells from cord blood	blood
21	chr6:37411200-37433200	Strong transcription	Fetal Intestine Small	intestine
22	chr6:37411400-37421800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr6:37411400-37427600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:37411400-37432200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:37411400-37433600	Strong transcription	Dnd41	blood
26	chr6:37411400-37437200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:37411600-37419200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:37411600-37421200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:37411600-37421200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:37411600-37421400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr6:37411600-37421400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr6:37411600-37421400	Strong transcription	Osteobl	bone
33	chr6:37411600-37421600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:37411600-37424800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:37411600-37427200	Strong transcription	Fetal Muscle Leg	muscle
36	chr6:37411600-37427800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:37411600-37431800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:37411600-37431800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr6:37411600-37432000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr6:37411600-37432000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:37411600-37432000	Strong transcription	Liver	Liver
42	chr6:37411600-37432000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr6:37411600-37432200	Strong transcription	Thymus	Thymus
44	chr6:37411600-37432800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr6:37411600-37433400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr6:37411600-37433400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:37411600-37436400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr6:37411800-37418400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:37411800-37419000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:37411800-37419000	Strong transcription	Brain Anterior Caudate	brain

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