Variant report

Variant	rs249428
Chromosome Location	chr5:40765721-40765722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40765278..40768665-chr5:40827361..40829681,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10056345	0.85[ASN][1000 genomes]
rs10060234	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10064175	0.81[ASN][1000 genomes]
rs1070446	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1097546	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355305	0.85[ASN][1000 genomes]
rs154268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154275	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154280	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154281	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154284	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171605	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171606	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs192219	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs193864	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193866	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2008763	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161521	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249413	0.85[ASN][1000 genomes]
rs249414	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs249416	0.87[ASN][1000 genomes]
rs249420	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249422	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249423	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249425	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249437	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249438	0.83[EUR][1000 genomes]
rs249441	0.80[ASN][1000 genomes]
rs257009	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569300	0.85[ASN][1000 genomes]
rs29740	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29742	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29743	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29744	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29761	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs323561	0.81[JPT][hapmap]
rs4277957	0.85[ASN][1000 genomes]
rs4285273	0.85[ASN][1000 genomes]
rs4315964	0.85[ASN][1000 genomes]
rs4315965	0.85[ASN][1000 genomes]
rs432071	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434778	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4383756	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs447810	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs453037	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457776	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs461404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466108	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466962	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.85[ASN][1000 genomes]
rs4957351	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59069340	0.85[ASN][1000 genomes]
rs59920139	0.85[ASN][1000 genomes]
rs6451535	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6451537	0.85[ASN][1000 genomes]
rs6871999	0.85[ASN][1000 genomes]
rs6896993	0.85[ASN][1000 genomes]
rs6897470	0.81[EUR][1000 genomes]
rs7708680	0.85[ASN][1000 genomes]
rs7711806	0.94[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726237	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs7737044	0.85[ASN][1000 genomes]
rs837101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs249428		cis	Lymphoblastoid	GTEx
rs249428	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs249428	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL
rs249428	TTC33	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756000-40776000	Weak transcription	Aorta	Aorta
2	chr5:40756000-40780600	Weak transcription	Spleen	Spleen
3	chr5:40756200-40766800	Weak transcription	Small Intestine	intestine
4	chr5:40756200-40775200	Weak transcription	Stomach Mucosa	stomach
5	chr5:40756200-40797200	Weak transcription	Gastric	stomach
6	chr5:40756400-40773800	Weak transcription	Lung	lung
7	chr5:40756400-40775000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:40756400-40776200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:40756400-40776400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:40756400-40776800	Weak transcription	Psoas Muscle	Psoas
11	chr5:40756400-40780600	Weak transcription	Esophagus	oesophagus
12	chr5:40756400-40785200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:40756600-40766400	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:40756600-40766800	Weak transcription	Brain Germinal Matrix	brain
16	chr5:40756600-40766800	Weak transcription	Left Ventricle	heart
17	chr5:40756600-40767600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:40756600-40770200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:40756600-40775800	Weak transcription	Fetal Heart	heart
20	chr5:40756600-40776000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:40756600-40780600	Weak transcription	Pancreas	Pancrea
22	chr5:40756600-40781200	Weak transcription	Fetal Brain Male	brain
23	chr5:40757200-40777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:40757400-40768600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:40757600-40773600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:40758200-40777000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:40758400-40777800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:40758800-40767800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:40759000-40776200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr5:40759400-40777000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:40759400-40777200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr5:40759600-40767800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr5:40759600-40776000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr5:40759800-40768200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:40759800-40769800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:40759800-40776000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:40760000-40777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:40760400-40776200	Strong transcription	Osteobl	bone
39	chr5:40760600-40769800	Strong transcription	Dnd41	blood
40	chr5:40760600-40770000	Strong transcription	Hela-S3	cervix
41	chr5:40760600-40776000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:40760600-40777600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr5:40760800-40768800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:40760800-40769600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:40760800-40777600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:40761000-40768600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:40761000-40775600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:40761200-40769600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:40761200-40776000	Strong transcription	Liver	Liver
50	chr5:40761400-40768400	Strong transcription	Placenta	Placenta

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