Variant report

Variant	rs10053664
Chromosome Location	chr5:40785811-40785812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40784492..40786831-chr5:40790905..40792585,2	MCF-7	breast:
2	chr5:40785220..40789232-chr5:40791780..40795190,3	K562	blood:
3	chr5:40783804..40787738-chr5:40796693..40801758,5	K562	blood:
4	chr5:40780330..40783240-chr5:40783326..40786085,3	K562	blood:
5	chr5:40780330..40782548-chr5:40784547..40786085,2	K562	blood:
6	chr5:40785737..40787489-chr5:40788508..40791029,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132356	Chromatin interaction
ENSG00000212567	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10035235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10062565	0.90[JPT][hapmap]
rs10066459	0.94[JPT][hapmap]
rs10069737	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1015027	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10941525	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11747210	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12514352	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12517210	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12520058	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12523329	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1363847	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2270625	0.90[JPT][hapmap]
rs2291782	0.90[JPT][hapmap]
rs3792824	0.90[ASN][1000 genomes]
rs3792827	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3805489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3805490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3805492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3805494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3805499	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3816959	0.90[JPT][hapmap];0.95[YRI][hapmap]
rs4957334	0.95[JPT][hapmap]
rs4957350	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357564	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6868112	0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6884484	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7719692	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7721093	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7725810	0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9800106	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10053664	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
4	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:40771600-40788600	Weak transcription	Fetal Stomach	stomach
6	chr5:40773000-40788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
8	chr5:40776600-40786200	Weak transcription	GM12878-XiMat	blood
9	chr5:40776600-40787600	Weak transcription	Hela-S3	cervix
10	chr5:40777000-40787800	Weak transcription	HMEC	breast
11	chr5:40777000-40788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:40777000-40788200	Weak transcription	Brain Anterior Caudate	brain
13	chr5:40777000-40789400	Weak transcription	Fetal Heart	heart
14	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
16	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:40777200-40786200	Weak transcription	K562	blood
19	chr5:40777200-40787800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:40777200-40787800	Weak transcription	Primary B cells from cord blood	blood
21	chr5:40777200-40787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:40777200-40788000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:40777200-40788000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:40777200-40788000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:40777200-40788200	Weak transcription	Primary T cells from cord blood	blood
26	chr5:40777200-40788200	Weak transcription	Dnd41	blood
27	chr5:40777200-40791400	Weak transcription	Brain Angular Gyrus	brain
28	chr5:40777200-40796000	Weak transcription	Lung	lung
29	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
30	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:40777400-40787800	Weak transcription	Fetal Brain Female	brain
32	chr5:40777600-40788400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:40777600-40789400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr5:40777600-40792000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:40777600-40792800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:40777600-40795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:40777600-40795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:40777800-40788400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:40777800-40789600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr5:40777800-40795600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:40777800-40796600	Weak transcription	NH-A	brain
42	chr5:40778000-40795400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:40778400-40786600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:40780800-40786200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:40781000-40786800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:40781000-40791200	Weak transcription	NHEK	skin
47	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
48	chr5:40781200-40787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:40782400-40787600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:40782400-40788400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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