Variant report

Variant	rs29743
Chromosome Location	chr5:40755280-40755281
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
2	chr5:40752902..40758440-chr5:40826185..40833524,16	K562	blood:
3	chr5:40754825..40755698-chr6:35227582..35228201,2	Hela-S3	cervix:
4	chr12:123011071..123011668-chr5:40755069..40755697,2	Hela-S3	cervix:
5	chr5:40745599..40747692-chr5:40753558..40755440,2	MCF-7	breast:
6	chr5:40754836..40755851-chr5:40878943..40880145,7	K562	blood:
7	chr5:40753427..40755619-chr5:40793452..40795341,2	K562	blood:
8	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
9	chr5:40753675..40755359-chr5:40838537..40842271,3	K562	blood:
10	chr5:40755135..40755798-chr5:40797964..40799024,4	MCF-7	breast:
11	chr5:40753631..40759305-chr5:40833742..40838306,12	K562	blood:
12	chr5:40749464..40751000-chr5:40753765..40756000,2	K562	blood:
13	chr5:40753789..40755953-chr5:40763164..40764930,2	K562	blood:
14	chr5:40753823..40758906-chr5:40833676..40836936,8	MCF-7	breast:
15	chr5:40754814..40759259-chr5:40796869..40798614,4	MCF-7	breast:
16	chr5:40752681..40758776-chr5:40831589..40836413,12	MCF-7	breast:
17	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
18	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
19	chr5:40753845..40758533-chr5:40769118..40772000,4	K562	blood:
20	chr5:40755051..40755677-chr5:40904503..40905135,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132357	Chromatin interaction
ENSG00000111011	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000212296	Chromatin interaction
ENSG00000132356	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10056345	0.85[ASN][1000 genomes]
rs10060234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs10064175	0.81[ASN][1000 genomes]
rs1057631	0.84[CEU][hapmap]
rs1070446	0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs10737963	0.83[CEU][hapmap]
rs1097546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355305	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs154268	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154275	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]
rs154280	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154281	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154284	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171606	0.92[ASN][1000 genomes]
rs192219	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs193864	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193866	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2008763	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161521	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249413	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249416	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249420	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249423	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249428	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]
rs249429	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249437	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249441	0.80[ASN][1000 genomes]
rs257009	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569300	0.85[ASN][1000 genomes]
rs29740	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29761	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs4133101	0.88[CEU][hapmap]
rs4277957	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4285273	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4315964	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4315965	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs432071	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345353	0.84[CEU][hapmap]
rs434778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4383756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs4434423	0.84[CEU][hapmap];0.85[YRI][hapmap]
rs447810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs453037	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546432	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs4573034	0.82[EUR][1000 genomes]
rs457776	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4607392	0.88[CEU][hapmap]
rs461404	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466108	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466962	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59069340	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59920139	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6451535	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs6451537	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6871999	0.85[ASN][1000 genomes]
rs6896993	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7708680	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7711806	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs7737044	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs837101	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[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
rs29743	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs29743	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs29743	RPL37	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40742000-40755400	Weak transcription	Spleen	Spleen
2	chr5:40754200-40756400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:40754200-40756600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:40754400-40755400	Active TSS	Brain Germinal Matrix	brain
5	chr5:40754400-40756200	Active TSS	Fetal Brain Male	brain
6	chr5:40754400-40756200	Active TSS	Thymus	Thymus
7	chr5:40754400-40756400	Active TSS	Ovary	ovary
8	chr5:40754400-40756600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:40754600-40756200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:40754600-40756200	Active TSS	Primary T cells fromperipheralblood	blood
11	chr5:40754600-40756200	Active TSS	Fetal Thymus	thymus
12	chr5:40754600-40756200	Active TSS	Right Atrium	heart
13	chr5:40754600-40756200	Active TSS	Stomach Smooth Muscle	stomach
14	chr5:40754600-40756400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr5:40754600-40756400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr5:40754600-40756400	Active TSS	Fetal Kidney	kidney
17	chr5:40754600-40756400	Active TSS	Psoas Muscle	Psoas
18	chr5:40754600-40756400	Active TSS	GM12878-XiMat	blood
19	chr5:40754600-40756600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:40754600-40756600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:40754600-40756600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:40754600-40756600	Active TSS	Fetal Intestine Large	intestine
23	chr5:40754600-40756600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr5:40754800-40755400	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr5:40754800-40755400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr5:40754800-40755400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:40754800-40755400	Flanking Active TSS	Liver	Liver
28	chr5:40754800-40756000	Active TSS	Aorta	Aorta
29	chr5:40754800-40756200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:40754800-40756200	Active TSS	Colonic Mucosa	Colon
31	chr5:40754800-40756200	Active TSS	Fetal Muscle Trunk	muscle
32	chr5:40754800-40756200	Active TSS	Fetal Stomach	stomach
33	chr5:40754800-40756200	Active TSS	Right Ventricle	heart
34	chr5:40754800-40756200	Active TSS	Stomach Mucosa	stomach
35	chr5:40754800-40756400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr5:40754800-40756400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:40754800-40756400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:40754800-40756400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr5:40754800-40756400	Active TSS	Brain Cingulate Gyrus	brain
40	chr5:40754800-40756400	Active TSS	Fetal Lung	lung
41	chr5:40754800-40756400	Active TSS	HSMMtube	muscle
42	chr5:40754800-40756400	Active TSS	NHDF-Ad	bronchial
43	chr5:40754800-40756600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:40754800-40756600	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr5:40754800-40756600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:40754800-40756600	Active TSS	Brain Hippocampus Middle	brain
47	chr5:40754800-40756600	Active TSS	NHEK	skin
48	chr5:40755000-40755400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:40755000-40755600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr5:40755000-40756000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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