Variant report

Variant	rs154275
Chromosome Location	chr5:40778641-40778642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40778589..40781225-chr5:40798736..40800242,2	K562	blood:
2	chr5:40776383..40778845-chr5:40780186..40782219,2	K562	blood:
3	chr5:40776154..40778816-chr5:40827762..40829741,2	K562	blood:
4	chr5:40778589..40781833-chr5:40798494..40800242,3	K562	blood:
5	chr5:40755924..40758676-chr5:40778215..40780297,2	K562	blood:
6	chr5:40776304..40779172-chr5:40780359..40783099,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113638	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10056345	0.85[ASN][1000 genomes]
rs10060234	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10064175	0.81[ASN][1000 genomes]
rs1070446	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs1097546	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155724	0.81[CEU][hapmap]
rs13167906	0.81[CEU][hapmap]
rs13355305	0.85[ASN][1000 genomes]
rs154268	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154280	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154281	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154284	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171605	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171606	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs192219	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs193864	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193866	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2008763	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161521	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249413	0.85[ASN][1000 genomes]
rs249414	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs249416	0.87[ASN][1000 genomes]
rs249420	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249422	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249423	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249425	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249428	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]
rs249429	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249437	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249438	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs249441	0.80[ASN][1000 genomes]
rs257009	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569300	0.85[ASN][1000 genomes]
rs29740	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29742	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29743	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29744	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29761	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434778	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs4383756	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs447810	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs453037	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457776	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs461404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466108	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466962	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.85[ASN][1000 genomes]
rs4957351	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59069340	0.85[ASN][1000 genomes]
rs59920139	0.85[ASN][1000 genomes]
rs6451535	0.87[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][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	0.82[EUR][1000 genomes]
rs7708680	0.85[ASN][1000 genomes]
rs7711806	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726237	0.87[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs7737044	0.85[ASN][1000 genomes]
rs837101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs154275	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs154275	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs154275	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756000-40780600	Weak transcription	Spleen	Spleen
2	chr5:40756200-40797200	Weak transcription	Gastric	stomach
3	chr5:40756400-40780600	Weak transcription	Esophagus	oesophagus
4	chr5:40756400-40785200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:40756600-40780600	Weak transcription	Pancreas	Pancrea
7	chr5:40756600-40781200	Weak transcription	Fetal Brain Male	brain
8	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
9	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:40766000-40782200	Weak transcription	Brain Substantia Nigra	brain
11	chr5:40769800-40779000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:40771600-40788600	Weak transcription	Fetal Stomach	stomach
13	chr5:40771800-40781400	Weak transcription	HSMMtube	muscle
14	chr5:40773000-40788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:40774400-40780800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:40774800-40782200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:40776200-40782000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
19	chr5:40776400-40781800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:40776400-40782000	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:40776400-40784800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:40776600-40779600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:40776600-40782000	Weak transcription	Small Intestine	intestine
24	chr5:40776600-40786200	Weak transcription	GM12878-XiMat	blood
25	chr5:40776600-40787600	Weak transcription	Hela-S3	cervix
26	chr5:40776800-40779200	Weak transcription	Placenta	Placenta
27	chr5:40776800-40781000	Weak transcription	NHDF-Ad	bronchial
28	chr5:40776800-40782000	Weak transcription	Brain Germinal Matrix	brain
29	chr5:40776800-40782800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:40776800-40784600	Weak transcription	HUVEC	blood vessel
31	chr5:40777000-40778800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:40777000-40779000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:40777000-40779800	Weak transcription	HepG2	liver
34	chr5:40777000-40780400	Weak transcription	A549	lung
35	chr5:40777000-40780400	Weak transcription	NHEK	skin
36	chr5:40777000-40780600	Weak transcription	Aorta	Aorta
37	chr5:40777000-40780600	Weak transcription	Left Ventricle	heart
38	chr5:40777000-40780800	Weak transcription	Adipose Nuclei	Adipose
39	chr5:40777000-40781600	Weak transcription	HSMM	muscle
40	chr5:40777000-40781800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:40777000-40781800	Weak transcription	NHLF	lung
42	chr5:40777000-40782000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:40777000-40782000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:40777000-40782000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:40777000-40782000	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:40777000-40782000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr5:40777000-40782000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:40777000-40782000	Weak transcription	Fetal Lung	lung
49	chr5:40777000-40782000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:40777000-40782200	Weak transcription	Brain Cingulate Gyrus	brain

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