Variant report

Variant	rs4383756
Chromosome Location	chr5:40689000-40689001
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:39713214..39716525-chr5:40687995..40689970,3	MCF-7	breast:
2	chr5:40677704..40682849-chr5:40683671..40689280,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10056345	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064175	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1057631	0.84[CEU][hapmap]
rs1070446	0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs10737963	0.83[CEU][hapmap]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13355305	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs154268	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs154275	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]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs171605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs192219	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs193864	0.83[ASN][1000 genomes]
rs193866	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2161521	0.85[ASN][1000 genomes]
rs249413	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs249414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249416	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249420	0.83[ASN][1000 genomes]
rs249422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs249423	0.85[ASN][1000 genomes]
rs249425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs249428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs249429	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs257009	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs28569300	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs29743	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]
rs29744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs29761	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs369940	0.80[AMR][1000 genomes]
rs4133101	0.88[CEU][hapmap]
rs4277957	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4285273	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315964	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315965	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs432071	0.85[ASN][1000 genomes]
rs4345353	0.84[CEU][hapmap]
rs434778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4434423	0.84[CEU][hapmap]
rs447810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs453037	0.85[ASN][1000 genomes]
rs4546432	0.87[CEU][hapmap]
rs4573034	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs457776	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4607392	0.88[CEU][hapmap]
rs461404	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs466108	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs466962	0.83[ASN][1000 genomes]
rs4957344	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59069340	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59920139	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451535	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451537	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6869461	0.81[AMR][1000 genomes]
rs6871999	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896993	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708680	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711806	0.93[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs7726237	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7733162	0.82[AMR][1000 genomes]
rs7737044	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs837101	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.84[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	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4383756	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs4383756	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs4383756	RPL37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40679000-40689400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:40680200-40689600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr5:40680800-40690800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr5:40682400-40691400	Weak transcription	Spleen	Spleen
5	chr5:40682800-40691400	Weak transcription	Lung	lung
6	chr5:40683000-40691600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:40683000-40691600	Weak transcription	Esophagus	oesophagus
8	chr5:40683000-40692000	Weak transcription	Gastric	stomach
9	chr5:40683800-40690200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:40683800-40691600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:40684000-40690200	Weak transcription	Pancreas	Pancrea
12	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
13	chr5:40684600-40691600	Weak transcription	Fetal Stomach	stomach
14	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
15	chr5:40685400-40690400	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:40685400-40691800	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:40685400-40692000	Weak transcription	Aorta	Aorta
18	chr5:40685600-40690800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr5:40685800-40691600	Weak transcription	Colonic Mucosa	Colon
20	chr5:40686400-40690200	Weak transcription	Fetal Intestine Small	intestine
21	chr5:40686400-40690600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:40686800-40690800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:40686800-40692000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:40687000-40690000	Enhancers	Colon Smooth Muscle	Colon
25	chr5:40687400-40690400	Genic enhancers	HSMM	muscle
26	chr5:40687600-40690600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:40687600-40690600	Enhancers	HMEC	breast
28	chr5:40687800-40689000	Enhancers	Primary B cells from cord blood	blood
29	chr5:40687800-40690200	Enhancers	Osteobl	bone
30	chr5:40687800-40690600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:40687800-40691800	Weak transcription	Small Intestine	intestine
32	chr5:40688000-40689200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:40688000-40689600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr5:40688000-40689600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr5:40688000-40689800	Enhancers	Hela-S3	cervix
36	chr5:40688000-40690000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:40688000-40690400	Enhancers	NH-A	brain
38	chr5:40688000-40691600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:40688200-40689000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:40688200-40689000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr5:40688200-40689200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr5:40688200-40689200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:40688200-40689200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:40688200-40689400	Enhancers	NHEK	skin
45	chr5:40688200-40690600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:40688200-40691000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr5:40688200-40693800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr5:40688400-40689000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:40688400-40689200	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:40688400-40689200	Genic enhancers	Muscle Satellite Cultured Cells	--

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